diff --git a/.gitmodules b/.gitmodules
index 83479b686a..fc7d7ce569 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -124,42 +124,42 @@ fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = v3.0.0
+fxtag = v3.0.1
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.63
+fxtag = ccs_config_cesm1.0.65
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.135
+fxtag = cime6.1.144
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.1.23
+fxtag = cmeps1.1.24
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.83
+fxtag = cdeps1.0.84
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.9
+fxtag = share1.1.16
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
@@ -194,6 +194,6 @@ fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
 [submodule "tools/CUPiD"]
 path = tools/CUPiD
 url = https://github.com/NCAR/CUPiD.git
-fxtag = v0.3.1
+fxtag = v0.4.0
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml
index 6cb8102b94..1d8d10f544 100644
--- a/.lib/git-fleximod/.github/workflows/pytest.yaml
+++ b/.lib/git-fleximod/.github/workflows/pytest.yaml
@@ -73,8 +73,7 @@ jobs:
       - run: |
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-          poetry run pytest
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
+          poetry run pytest --doctest-modules
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3
diff --git a/.lib/git-fleximod/.pre-commit-config.yaml b/.lib/git-fleximod/.pre-commit-config.yaml
index 2f6089da72..fc6ec61b6f 100644
--- a/.lib/git-fleximod/.pre-commit-config.yaml
+++ b/.lib/git-fleximod/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ exclude: ^utils/.*$
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
diff --git a/.lib/git-fleximod/CODE_OF_CONDUCT.md b/.lib/git-fleximod/CODE_OF_CONDUCT.md
index 84f2925bba..f2c52d5b77 100644
--- a/.lib/git-fleximod/CODE_OF_CONDUCT.md
+++ b/.lib/git-fleximod/CODE_OF_CONDUCT.md
@@ -17,7 +17,7 @@ Examples of behaviors that contribute to a positive environment include:
 * Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism
 * Acknowledging the contributions of others
 * Avoid personal attacks directed toward other participants
-* Be mindful of your surroundings and of your fellow participants 
+* Be mindful of your surroundings and of your fellow participants
 * Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress
 * Respect the rules and policies of the project and venue
 
@@ -29,7 +29,7 @@ Examples of unacceptable behavior include, but are not limited to:
 * Personal attacks directed at other guests, members, participants, etc.
 * Publishing others' private information, such as a physical or electronic address, without explicit permission
 * Alarming, intimidating, threatening, or hostile comments or conduct
-* Inappropriate use of nudity and/or sexual images 
+* Inappropriate use of nudity and/or sexual images
 * Threatening or stalking anyone, including a participant
 * Other conduct which could reasonably be considered inappropriate in a professional setting
 
@@ -60,7 +60,7 @@ the [Attribution](#attribution) section.
 ## Reporting
 Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as
 outlined in the [Consequences](#consequences) section below.
-However, making a report to a project administrator is not considered an 'official report' to UCAR. 
+However, making a report to a project administrator is not considered an 'official report' to UCAR.
 
 Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint
 Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's
diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
index e4acc55582..9551bc96b8 100644
--- a/.lib/git-fleximod/git_fleximod/cli.py
+++ b/.lib/git-fleximod/git_fleximod/cli.py
@@ -1,8 +1,8 @@
 from pathlib import Path
 import argparse, os, sys
-from git_fleximod import utils
 
-__version__ = "1.0.3"
+__version__ = "1.1.1"
+
 
 class CustomArgumentParser(argparse.ArgumentParser):
     def print_help(self, file=None):
@@ -17,13 +17,28 @@ def print_help(self, file=None):
         for path in candidate_paths:
             if os.path.exists(path):
                 with open(path) as f:
-                    print( f.read(), file=file)
+                    print(f.read(), file=file)
                     return
-        print( "README.md not found.", file=file)
+        print("README.md not found.", file=file)
+
 
 def find_root_dir(filename=".gitmodules"):
-    """ finds the highest directory in tree
-    which contains a file called filename """
+    """
+    Finds the highest directory in tree which contains a file called filename.
+
+    >>> import tempfile, os
+    >>> cwd = os.getcwd()
+    >>> with tempfile.TemporaryDirectory() as tmp:
+    ...     subdir = Path(tmp) / 'subdir'
+    ...     subdir.mkdir()
+    ...     f = Path(tmp) / '.gitmodules'
+    ...     _ = f.write_text('')
+    ...     os.chdir(subdir)
+    ...     result = find_root_dir('.gitmodules') == str(tmp)
+    ...     os.chdir(cwd)
+    ...     result
+    True
+    """
     d = Path.cwd()
     root = Path(d.root)
     dirlist = []
@@ -40,6 +55,7 @@ def find_root_dir(filename=".gitmodules"):
             return str(dl)
     return None
 
+
 def get_parser():
     description = """
     %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models
@@ -116,6 +132,13 @@ def get_parser():
         "verbosity level each time.",
     )
 
+    parser.add_argument(
+        "--no-mods-details",
+        action="store_true",
+        default=False,
+        help="Suppress details on local mods in status output.",
+    )
+
     parser.add_argument(
         "-V",
         "--version",
diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py
index b3c4fece4e..ce63b8bd10 100755
--- a/.lib/git-fleximod/git_fleximod/git_fleximod.py
+++ b/.lib/git-fleximod/git_fleximod/git_fleximod.py
@@ -7,21 +7,27 @@
 
 import os
 import shutil
-import logging
-import textwrap
 import asyncio
+import logging
+from configparser import NoOptionError
 from git_fleximod import utils
 from git_fleximod import cli
 from git_fleximod.gitinterface import GitInterface
 from git_fleximod.gitmodules import GitModules
 from git_fleximod.submodule import Submodule
 
-# logger variable is global
-logger = None
+logger = logging.getLogger(__name__)
 
 
 def fxrequired_allowed_values():
-    return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional", "TopLevelRequired", "TopLevelOptional"]
+    return [
+        "ToplevelRequired",
+        "ToplevelOptional",
+        "AlwaysRequired",
+        "AlwaysOptional",
+        "TopLevelRequired",
+        "TopLevelOptional",
+    ]
 
 
 def commandline_arguments(args=None):
@@ -69,6 +75,7 @@ def commandline_arguments(args=None):
         options.components,
         options.exclude,
         options.force,
+        options.no_mods_details,
         action,
     )
 
@@ -151,8 +158,8 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
 
     if os.path.isdir(os.path.join(root_dir, path, ".git")):
         with utils.pushd(sprep_repo):
-            if os.path.isdir(os.path.join(topgit,".git")):
-                shutil.rmtree(os.path.join(topgit,".git"))
+            if os.path.isdir(os.path.join(topgit, ".git")):
+                shutil.rmtree(os.path.join(topgit, ".git"))
             shutil.move(".git", topgit)
             with open(".git", "w") as f:
                 f.write("gitdir: " + os.path.relpath(topgit))
@@ -167,7 +174,6 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
         with utils.pushd(sprep_repo):
             if os.path.isfile(sparsefile):
                 shutil.copy(sparsefile, gitsparse)
-                
 
     # Finally checkout the repo
     sprepo_git.git_operation("fetch", "origin", "--tags")
@@ -177,7 +183,8 @@ def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master
     rgit.config_set_value(f'submodule "{name}"', "active", "true")
     rgit.config_set_value(f'submodule "{name}"', "url", url)
 
-def init_submodule_from_gitmodules(gitmodules, name, root_dir, logger):
+
+def init_submodule_from_gitmodules(gitmodules, name, root_dir, llogger):
     path = gitmodules.get(name, "path")
     url = gitmodules.get(name, "url")
     assert path and url, f"Malformed .gitmodules file {path} {url}"
@@ -187,60 +194,73 @@ def init_submodule_from_gitmodules(gitmodules, name, root_dir, logger):
     fxurl = gitmodules.get(name, "fxDONOTUSEurl")
     fxsparse = gitmodules.get(name, "fxsparse")
     fxrequired = gitmodules.get(name, "fxrequired")
-    return Submodule(root_dir, name, path, url, fxtag=tag, fxurl=fxurl, fxsparse=fxsparse, fxrequired=fxrequired, logger=logger)
+    return Submodule(
+        root_dir,
+        name,
+        path,
+        url,
+        fxtag=tag,
+        fxurl=fxurl,
+        fxsparse=fxsparse,
+        fxrequired=fxrequired,
+        logger=llogger,
+    )
 
-def submodules_status(gitmodules, root_dir, toplevel=False, depth=0):
+
+def submodules_status(
+    gitmodules, root_dir, toplevel=False, depth=0, no_mods_details=False
+):
     testfails = 0
     localmods = 0
     needsupdate = 0
-    wrapper = textwrap.TextWrapper(initial_indent=' '*(depth*10), width=120,subsequent_indent=' '*(depth*20))
     for name in gitmodules.sections():
         submod = init_submodule_from_gitmodules(gitmodules, name, root_dir, logger)
-            
-        result,n,l,t = submod.status()
+
+        result, n, l, t = submod.status(depth=depth, no_mods_details=no_mods_details)
         if toplevel or not submod.toplevel():
-            print(wrapper.fill(result))
+            print(result)
             testfails += t
             localmods += l
             needsupdate += n
         subdir = os.path.join(root_dir, submod.path)
         if os.path.exists(os.path.join(subdir, ".gitmodules")):
             gsubmod = GitModules(logger, confpath=subdir)
-            t,l,n = submodules_status(gsubmod, subdir, depth=depth+1)
+            t, l, n = submodules_status(
+                gsubmod, subdir, depth=depth + 1, no_mods_details=no_mods_details
+            )
             if toplevel or not submod.toplevel():
                 testfails += t
                 localmods += l
                 needsupdate += n
-            
+
     return testfails, localmods, needsupdate
 
-def git_toplevelroot(root_dir, logger):
-    rgit = GitInterface(root_dir, logger)
+
+def git_toplevelroot(root_dir, llogger):
+    rgit = GitInterface(root_dir, llogger)
     _, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
     return superroot
 
+
 async def submodules_update(gitmodules, root_dir, requiredlist, force):
     async def update_submodule(name, requiredlist, force):
         submod = init_submodule_from_gitmodules(gitmodules, name, root_dir, logger)
 
-        _, needsupdate, localmods, testfails = submod.status()
         if not submod.fxrequired:
             submod.fxrequired = "AlwaysRequired"
-        fxrequired = submod.fxrequired    
+        fxrequired = submod.fxrequired
         allowedvalues = fxrequired_allowed_values()
         assert fxrequired in allowedvalues
 
         superroot = git_toplevelroot(root_dir, logger)
-                                     
-        if (
-            fxrequired
-            and ((superroot and "Toplevel" in fxrequired)
-            or fxrequired not in requiredlist)
+
+        if fxrequired and (
+            (superroot and "Toplevel" in fxrequired) or fxrequired not in requiredlist
         ):
             if "Optional" in fxrequired and "Optional" not in requiredlist:
                 if fxrequired.startswith("Always"):
                     print(f"Skipping optional component {name:>20}")
-                return # continue to next submodule
+                return  # continue to next submodule
         optional = "AlwaysOptional" in requiredlist
 
         if fxrequired in requiredlist:
@@ -253,11 +273,16 @@ async def update_submodule(name, requiredlist, force):
                 newrequiredlist = ["AlwaysRequired"]
                 if optional:
                     newrequiredlist.append("AlwaysOptional")
-                await submodules_update(gitsubmodules, repodir, newrequiredlist, force=force)
+                await submodules_update(
+                    gitsubmodules, repodir, newrequiredlist, force=force
+                )
 
-    tasks = [update_submodule(name, requiredlist, force) for name in gitmodules.sections()]
+    tasks = [
+        update_submodule(name, requiredlist, force) for name in gitmodules.sections()
+    ]
     await asyncio.gather(*tasks)
 
+
 def local_mods_output():
     text = """\
     The submodules labeled with 'M' above are not in a clean state.
@@ -271,7 +296,8 @@ def local_mods_output():
 """
     print(text)
 
-def submodules_test(gitmodules, root_dir):
+
+def submodules_test(gitmodules, root_dir, no_mods_details=False):
     """
     This function tests the git submodules based on the provided parameters.
 
@@ -282,12 +308,15 @@ def submodules_test(gitmodules, root_dir):
     Parameters:
     gitmodules (ConfigParser): The gitmodules configuration.
     root_dir (str): The root directory for the git operation.
+    no_mods_details (bool, optional): If True, suppress details on local mods in status output
 
     Returns:
     int: The number of test failures.
     """
     # First check that fxtags are present and in sync with submodule hashes
-    testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir)
+    testfails, localmods, needsupdate = submodules_status(
+        gitmodules, root_dir, no_mods_details=no_mods_details
+    )
     print("")
     # Then make sure that urls are consistant with fxurls (not forks and not ssh)
     # and that sparse checkout files exist
@@ -315,14 +344,17 @@ def main():
         includelist,
         excludelist,
         force,
+        no_mods_details,
         action,
     ) = commandline_arguments()
     # Get a logger for the package
     global logger
     logger = logging.getLogger(__name__)
 
-    logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name))
-    
+    logger.info(
+        "action is {} root_dir={} file_name={}".format(action, root_dir, file_name)
+    )
+
     if not root_dir or not os.path.isfile(os.path.join(root_dir, file_name)):
         if root_dir:
             file_path = utils.find_upwards(root_dir, file_name)
@@ -352,7 +384,9 @@ def main():
     if action == "update":
         asyncio.run(submodules_update(gitmodules, root_dir, fxrequired, force))
     elif action == "status":
-        tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True)
+        tfails, lmods, updates = submodules_status(
+            gitmodules, root_dir, toplevel=True, no_mods_details=no_mods_details
+        )
         if tfails + lmods + updates > 0:
             print(
                 f"    testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n"
@@ -360,7 +394,7 @@ def main():
             if lmods > 0:
                 local_mods_output()
     elif action == "test":
-        retval = submodules_test(gitmodules, root_dir)
+        retval = submodules_test(gitmodules, root_dir, no_mods_details=no_mods_details)
     else:
         utils.fatal_error(f"unrecognized action request {action}")
     return retval
diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py
index 022426d28c..cdd99748b5 100644
--- a/.lib/git-fleximod/git_fleximod/gitinterface.py
+++ b/.lib/git-fleximod/git_fleximod/gitinterface.py
@@ -1,19 +1,33 @@
-import os
+# git_fleximod/gitinterface.py
 import sys
 from . import utils
 from pathlib import Path
 import asyncio
 
+
 class GitInterface:
     def __init__(self, repo_path, logger):
-        logger.debug("Initialize GitInterface for {}".format(repo_path))
         if isinstance(repo_path, str):
             self.repo_path = Path(repo_path).resolve()
         elif isinstance(repo_path, Path):
             self.repo_path = repo_path.resolve()
         else:
             raise TypeError("repo_path must be a str or Path object")
-        self.logger = logger
+        if logger is not None:
+            self.logger = logger
+        else:
+            import logging
+
+            self.logger = logging.getLogger(__name__)
+            if not self.logger.hasHandlers():
+                handler = logging.StreamHandler()
+                formatter = logging.Formatter(
+                    "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+                )
+                handler.setFormatter(formatter)
+                self.logger.addHandler(handler)
+                self.logger.setLevel(logging.DEBUG)
+        self.logger.debug("Initialize GitInterface for {}".format(repo_path))
         try:
             import git
 
@@ -32,6 +46,12 @@ def __init__(self, repo_path, logger):
         self.logger.info(msg)
 
     def _git_command(self, operation, *args):
+        """
+        Internal: Build git command or call GitPython.
+        >>> gi = GitInterface('.', None)
+        >>> isinstance(gi._git_command('status'), list) or isinstance(gi._git_command('status'), str)
+        True
+        """
         self.logger.info(operation)
         if self._use_module and operation != "submodule":
             try:
@@ -60,6 +80,15 @@ def _git_operation_command(self, operation, args):
 
     # pylint: disable=unused-argument
     def git_operation(self, operation, *args, **kwargs):
+        """
+        Run a git operation and return status and output.
+        >>> gi = GitInterface('.', None)
+        >>> status, output = gi.git_operation('status')
+        >>> isinstance(status, int)
+        True
+        >>> isinstance(output, str)
+        True
+        """
         newargs = []
         for a in args:
             # Do not use ssh interface
@@ -70,7 +99,9 @@ def git_operation(self, operation, *args, **kwargs):
         command = self._git_command(operation, *newargs)
         if isinstance(command, list):
             try:
-                status, output = utils.execute_subprocess(command, status_to_caller=True, output_to_caller=True)
+                status, output = utils.execute_subprocess(
+                    command, status_to_caller=True, output_to_caller=True
+                )
                 return status, output.rstrip()
             except Exception as e:
                 sys.exit(e)
@@ -79,13 +110,17 @@ def git_operation(self, operation, *args, **kwargs):
 
     # pylint: disable=unused-argument
     async def git_operation_async(self, operation, *args, **kwargs):
+        """
+        Asynchronously run a git operation.
+        (Doc test not run: async context)
+        """
         command = self._git_operation_command(operation, args)
         if isinstance(command, list):
             try:
                 process = await asyncio.create_subprocess_exec(
                     *command,
                     stdout=asyncio.subprocess.PIPE,
-                    stderr=asyncio.subprocess.PIPE
+                    stderr=asyncio.subprocess.PIPE,
                 )
                 stdout, stderr = await process.communicate()
                 status = process.returncode
@@ -97,6 +132,12 @@ async def git_operation_async(self, operation, *args, **kwargs):
             return 0, command
 
     def config_get_value(self, section, name):
+        """
+        Get a git config value.
+        >>> gi = GitInterface('.', None)
+        >>> gi.config_get_value('user', 'name') is None or isinstance(gi.config_get_value('user', 'name'), str)
+        True
+        """
         if self._use_module:
             config = self.repo.config_reader()
             try:
@@ -105,18 +146,36 @@ def config_get_value(self, section, name):
                 val = None
             return val
         else:
-            cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}")
+            cmd = (
+                "git",
+                "-C",
+                str(self.repo_path),
+                "config",
+                "--get",
+                f"{section}.{name}",
+            )
             output = utils.execute_subprocess(cmd, output_to_caller=True)
             return output.strip()
 
     def config_set_value(self, section, name, value):
+        """
+        Set a git config value.
+        (Doc test not run: modifies config)
+        """
         if self._use_module:
             with self.repo.config_writer() as writer:
-                if "." in section:  
-                    section = section.replace("."," \"")+'"'           
+                if "." in section:
+                    section = section.replace(".", ' "') + '"'
                 writer.set_value(section, name, value)
             writer.release()  # Ensure changes are saved
         else:
-            cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value)
+            cmd = (
+                "git",
+                "-C",
+                str(self.repo_path),
+                "config",
+                f"{section}.{name}",
+                value,
+            )
             self.logger.info(cmd)
             utils.execute_subprocess(cmd, output_to_caller=True)
diff --git a/.lib/git-fleximod/git_fleximod/gitmodules.py b/.lib/git-fleximod/git_fleximod/gitmodules.py
index cf8b350dd6..7e02848970 100644
--- a/.lib/git-fleximod/git_fleximod/gitmodules.py
+++ b/.lib/git-fleximod/git_fleximod/gitmodules.py
@@ -1,4 +1,4 @@
-import shutil, os
+# git_fleximod/gitmodules.py
 from pathlib import Path
 from configparser import RawConfigParser, ConfigParser
 from .lstripreader import LstripReader
@@ -26,19 +26,18 @@ def __init__(
             )
         )
         super().__init__()
-        self.conf_file = (Path(confpath) / Path(conffile))
+        self.conf_file = Path(confpath) / Path(conffile)
         if self.conf_file.exists():
             self.read_file(LstripReader(str(self.conf_file)), source=conffile)
         self.includelist = includelist
         self.excludelist = excludelist
         self.isdirty = False
-        
+
     def reload(self):
         self.clear()
         if self.conf_file.exists():
             self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file)
 
-        
     def set(self, name, option, value):
         """
         Sets a configuration value for a specific submodule:
@@ -74,7 +73,7 @@ def save(self):
             with open(self.conf_file, "w") as fd:
                 self.write(fd)
         self.isdirty = False
-        
+
     def __del__(self):
         self.save()
 
diff --git a/.lib/git-fleximod/git_fleximod/metoflexi.py b/.lib/git-fleximod/git_fleximod/metoflexi.py
index cc347db2dd..d605b347f6 100755
--- a/.lib/git-fleximod/git_fleximod/metoflexi.py
+++ b/.lib/git-fleximod/git_fleximod/metoflexi.py
@@ -11,6 +11,7 @@
 
 logger = None
 
+
 def find_root_dir(filename=".git"):
     d = Path.cwd()
     root = Path(d.root)
@@ -30,10 +31,13 @@ def get_parser():
         description=description, formatter_class=argparse.RawDescriptionHelpFormatter
     )
 
-    parser.add_argument('-e', '--externals', nargs='?',
-                        default='Externals.cfg',
-                        help='The externals description filename. '
-                        'Default: %(default)s.')
+    parser.add_argument(
+        "-e",
+        "--externals",
+        nargs="?",
+        default="Externals.cfg",
+        help="The externals description filename. " "Default: %(default)s.",
+    )
 
     parser.add_argument(
         "-C",
@@ -70,6 +74,7 @@ def get_parser():
 
     return parser
 
+
 def commandline_arguments(args=None):
     parser = get_parser()
 
@@ -92,11 +97,8 @@ def commandline_arguments(args=None):
         level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers
     )
 
-    return(
-        options.path,
-        options.gitmodules,
-        options.externals
-        )
+    return (options.path, options.gitmodules, options.externals)
+
 
 class ExternalRepoTranslator:
     """
@@ -110,12 +112,13 @@ def __init__(self, rootpath, gitmodules, externals):
         self.externals = (rootpath / Path(externals)).resolve()
         print(f"Translating {self.externals}")
         self.git = GitInterface(rootpath, logger)
-        
-#    def __del__(self):
-#        if (self.rootpath / "save.gitignore"):
-            
 
-    def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol):
+    #    def __del__(self):
+    #        if (self.rootpath / "save.gitignore"):
+
+    def translate_single_repo(
+        self, section, tag, url, path, efile, hash_, sparse, protocol
+    ):
         """
         Translates a single repository based on configuration details.
 
@@ -145,13 +148,13 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
                 self.gitmodules.set(section, "fxtag", tag)
             if hash_:
                 self.gitmodules.set(section, "fxtag", hash_)
-            
+
             self.gitmodules.set(section, "fxDONOTUSEurl", url)
             if sparse:
                 self.gitmodules.set(section, "fxsparse", sparse)
             self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
         else:
-            newpath = (self.rootpath / Path(path))
+            newpath = self.rootpath / Path(path)
             if newpath.exists():
                 shutil.rmtree(newpath)
                 logger.info("Creating directory {}".format(newpath))
@@ -159,7 +162,9 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
             if tag:
                 logger.info("cloning {}".format(section))
                 try:
-                    self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path)
+                    self.git.git_operation(
+                        "clone", "-b", tag, "--depth", "1", url, path
+                    )
                 except:
                     self.git.git_operation("clone", url, path)
                     with utils.pushd(newpath):
@@ -172,27 +177,28 @@ def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, p
                 git.git_operation("checkout", hash_)
             if sparse:
                 print("setting as sparse submodule {}".format(section))
-                sparsefile = (newpath / Path(sparse))
-                newfile = (newpath / ".git" / "info" / "sparse-checkout")
+                sparsefile = newpath / Path(sparse)
+                newfile = newpath / ".git" / "info" / "sparse-checkout"
                 print(f"sparsefile {sparsefile} newfile {newfile}")
                 shutil.copy(sparsefile, newfile)
-        
-            logger.info("adding submodule {}".format(section))        
+
+            logger.info("adding submodule {}".format(section))
             self.gitmodules.save()
-            self.git.git_operation("submodule", "add", "-f", "--name", section, url, path)
-            self.git.git_operation("submodule","absorbgitdirs")
+            self.git.git_operation(
+                "submodule", "add", "-f", "--name", section, url, path
+            )
+            self.git.git_operation("submodule", "absorbgitdirs")
             self.gitmodules.reload()
             if tag:
                 self.gitmodules.set(section, "fxtag", tag)
             if hash_:
                 self.gitmodules.set(section, "fxtag", hash_)
-            
+
             self.gitmodules.set(section, "fxDONOTUSEurl", url)
             if sparse:
                 self.gitmodules.set(section, "fxsparse", sparse)
             self.gitmodules.set(section, "fxrequired", "ToplevelRequired")
-    
-        
+
     def translate_repo(self):
         """
         Translates external repositories defined within an external file.
@@ -218,8 +224,9 @@ def translate_repo(self):
             sparse = econfig.get(section, "sparse", raw=False, fallback=None)
             protocol = econfig.get(section, "protocol", raw=False, fallback=None)
 
-            self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol)
-
+            self.translate_single_repo(
+                section, tag, url, path, efile, hash_, sparse, protocol
+            )
 
 
 def _main():
@@ -231,6 +238,6 @@ def _main():
         logger.info("Translating {}".format(rootpath))
         t.translate_repo()
 
-        
+
 if __name__ == "__main__":
     sys.exit(_main())
diff --git a/.lib/git-fleximod/git_fleximod/submodule.py b/.lib/git-fleximod/git_fleximod/submodule.py
index 5a8c3f935e..b786ae9400 100644
--- a/.lib/git-fleximod/git_fleximod/submodule.py
+++ b/.lib/git-fleximod/git_fleximod/submodule.py
@@ -6,7 +6,8 @@
 from git_fleximod import utils
 from git_fleximod.gitinterface import GitInterface
 
-class Submodule():
+
+class Submodule:
     """
     Represents a Git submodule with enhanced features for flexible management.
 
@@ -21,9 +22,29 @@ class Submodule():
         fxrequired (str): Indicates if the submodule is optional or required (optional).
         logger (logging.Logger): Logger instance for logging (optional).
     """
-    def __init__(self, root_dir, name, path, url, fxtag=None, fxurl=None, fxsparse=None, fxrequired=None, logger=None):
+
+    def __init__(
+        self,
+        root_dir,
+        name,
+        path,
+        url,
+        fxtag=None,
+        fxurl=None,
+        fxsparse=None,
+        fxrequired=None,
+        logger=None,
+    ):
         """
         Initializes a new Submodule instance with the provided attributes.
+
+        >>> sm = Submodule('.', 'foo', 'bar', 'https://example.com')
+        >>> sm.name
+        'foo'
+        >>> sm.path
+        'bar'
+        >>> sm.url
+        'https://example.com'
         """
         self.name = name
         self.root_dir = root_dir
@@ -38,13 +59,19 @@ def __init__(self, root_dir, name, path, url, fxtag=None, fxurl=None, fxsparse=N
             self.fxrequired = "AlwaysRequired"
         self.logger = logger
 
-    def status(self):
+    def status(self, depth=0, no_mods_details=False):
         """
         Checks the status of the submodule and returns 4 parameters:
         - result (str): The status of the submodule.
         - needsupdate (bool): An indicator if the submodule needs to be updated.
         - localmods (bool): An indicator if the submodule has local modifications.
         - testfails (bool): An indicator if the submodule has failed a test, this is used for testing purposes.
+
+        Args:
+            depth (int, optional): depth of this submodule relative to root, used to
+                                   indent output for nested submodules
+            no_mods_details (bool, optional): if True, suppress details on local mods in
+                                              status output
         """
 
         smpath = os.path.join(self.root_dir, self.path)
@@ -52,16 +79,27 @@ def status(self):
         localmods = False
         needsupdate = False
         ahash = None
+
+        # The following prefix gives a tree-like output:
+        tree_prefix_spaces = 3
+        if depth == 0:
+            tree_prefix = ""
+        else:
+            tree_prefix = " " * tree_prefix_spaces * (depth - 1) + "└─ "
+
+        full_name = tree_prefix + self.name
+        name_width = 20
+        full_width = name_width + len(tree_prefix)
+
         optional = ""
         if "Optional" in self.fxrequired:
             optional = " (optional)"
-        required = None
-        level = None
+
         if not os.path.exists(os.path.join(smpath, ".git")):
             rootgit = GitInterface(self.root_dir, self.logger)
             # submodule commands use path, not name
-            status, tags = rootgit.git_operation("ls-remote", "--tags", self.url)
-            status, result = rootgit.git_operation("submodule","status",smpath)
+            _, tags = rootgit.git_operation("ls-remote", "--tags", self.url)
+            _, result = rootgit.git_operation("submodule", "status", smpath)
             result = result.split()
 
             if result:
@@ -69,7 +107,7 @@ def status(self):
             hhash = None
             atag = None
             for htag in tags.split("\n"):
-                if htag.endswith('^{}'):
+                if htag.endswith("^{}"):
                     htag = htag[:-3]
                 if ahash and not atag and ahash in htag:
                     atag = (htag.split()[1])[10:]
@@ -78,84 +116,139 @@ def status(self):
                 if hhash and atag:
                     break
             if self.fxtag and (ahash == hhash or atag == self.fxtag):
-                result = f"e {self.name:>20} not checked out, aligned at tag {self.fxtag}{optional}"
+                result = f"e  {full_name:<{full_width}} not checked out, aligned at tag {self.fxtag}{optional}"
                 needsupdate = True
             elif self.fxtag:
-                status, ahash = rootgit.git_operation(
+                _, ahash = rootgit.git_operation(
                     "submodule", "status", "{}".format(self.path)
                 )
                 ahash = ahash[1 : len(self.fxtag) + 1]
                 if self.fxtag == ahash:
-                    result = f"e {self.name:>20} not checked out, aligned at hash {ahash}{optional}"
+                    result = f"e  {full_name:<{full_width}} not checked out, aligned at hash {ahash}{optional}"
                 else:
-                    result = f"e {self.name:>20} not checked out, out of sync at tag {atag}, expected tag is {self.fxtag}{optional}"
+                    result = f"e  {full_name:<{full_width}} not checked out, out of sync at tag {atag}, expected tag is {self.fxtag}{optional}"
                     testfails = True
                 needsupdate = True
             else:
-                result = f"e {self.name:>20} has no fxtag defined in .gitmodules{optional}"
+                result = f"e  {full_name:<{full_width}} has no fxtag defined in .gitmodules{optional}"
                 testfails = False
         else:
             with utils.pushd(smpath):
                 git = GitInterface(smpath, self.logger)
-                status, remote = git.git_operation("remote")
-                if remote == '':
-                    result = f"e {self.name:>20} has no associated remote"
+                _, remote = git.git_operation("remote")
+                if remote == "":
+                    result = f"e  {full_name:<{full_width}} has no associated remote"
                     testfails = True
                     needsupdate = True
                     return result, needsupdate, localmods, testfails
-                status, rurl = git.git_operation("ls-remote","--get-url")
-                status, lines = git.git_operation("log", "--pretty=format:\"%h %d\"")
-                line = lines.partition('\n')[0]
+                _, rurl = git.git_operation("ls-remote", "--get-url")
+                _, lines = git.git_operation("log", '--pretty=format:"%h %d"')
+                line = lines.partition("\n")[0]
                 parts = line.split()
                 ahash = parts[0][1:]
                 atag = None
                 if len(parts) > 3:
                     idx = 0
-                    while idx < len(parts)-1:
-                        idx = idx+1
-                        if parts[idx] == 'tag:':
-                            atag = parts[idx+1]
-                            while atag.endswith(')') or atag.endswith(',') or atag.endswith("\""):
+                    while idx < len(parts) - 1:
+                        idx = idx + 1
+                        if parts[idx] == "tag:":
+                            atag = parts[idx + 1]
+                            while (
+                                atag.endswith(")")
+                                or atag.endswith(",")
+                                or atag.endswith('"')
+                            ):
                                 atag = atag[:-1]
                             if atag == self.fxtag:
                                 break
-                recurse = False
+
                 if rurl != self.url:
                     remote = self._add_remote(git)
                     git.git_operation("fetch", remote)
+
+                mod_char = " "
+                _, status_output = git.git_operation(
+                    "status", "--ignore-submodules", "-uno"
+                )
+                if "nothing to commit" not in status_output:
+                    localmods = True
+                    mod_char = "M"
+
                 # Asked for a tag and found that tag
                 if self.fxtag and atag == self.fxtag:
-                    result = f"  {self.name:>20} at tag {self.fxtag}"
-                    recurse = True
+                    result = (
+                        f" {mod_char} {full_name:<{full_width}} at tag {self.fxtag}"
+                    )
                     testfails = False
                 # Asked for and found a hash
-                elif self.fxtag and (ahash[: len(self.fxtag)] == self.fxtag or (self.fxtag.find(ahash)==0)):
-                    result = f"  {self.name:>20} at hash {ahash}"
-                    recurse = True
+                elif self.fxtag and (
+                    ahash[: len(self.fxtag)] == self.fxtag
+                    or (self.fxtag.find(ahash) == 0)
+                ):
+                    result = f" {mod_char} {full_name:<{full_width}} at hash {ahash}"
+
                     testfails = False
                 # Asked for and found a hash
                 elif atag == ahash:
-                    result = f"  {self.name:>20} at hash {ahash}"
-                    recurse = True
+                    result = f" {mod_char} {full_name:<{full_width}} at hash {ahash}"
+
                 # Did not find requested tag or hash
                 elif self.fxtag:
-                    result = f"s {self.name:>20} {atag} {ahash} is out of sync with .gitmodules {self.fxtag}"
+                    result = f"s{mod_char} {full_name:<{full_width}} {atag} {ahash} is out of sync with .gitmodules {self.fxtag}"
                     testfails = True
                     needsupdate = True
                 else:
                     if atag:
-                        result = f"e {self.name:>20} has no fxtag defined in .gitmodules, module at {atag}"
+                        result = f"e{mod_char} {full_name:<{full_width}} has no fxtag defined in .gitmodules, module at {atag}"
                     else:
-                        result = f"e {self.name:>20} has no fxtag defined in .gitmodules, module at {ahash}"
+                        result = f"e{mod_char} {full_name:<{full_width}} has no fxtag defined in .gitmodules, module at {ahash}"
                     testfails = False
 
-                status, output = git.git_operation("status", "--ignore-submodules", "-uno")
-                if "nothing to commit" not in output:
-                    localmods = True
-                    result = "M" + textwrap.indent(output, "                      ")
-#        print(f"result {result} needsupdate {needsupdate} localmods {localmods} testfails {testfails}")
-        return result, needsupdate, localmods, testfails
+                if localmods and not no_mods_details:
+                    # Print details about the local mods, indented below the other
+                    # information about this submodule.
+                    #
+                    # We use a vertical bar to help with the visual alignment of child
+                    # submodules. There are two main goals of the spacing details here:
+                    # 1. If there is a child of this submodule, the vertical bar used here
+                    #    should connect with the vertical part of the tree_prefix.
+                    # 2. The details about any local mods should be indented an additional
+                    #    4 spaces beyond the start of the text like "at tag ..."
+                    #
+                    # Here are details on how we accomplish these goals:
+                    # - leading_spaces: This is key for accomplishing the first goal. We
+                    #   need 3 spaces for the first three characters in the output (two
+                    #   status characters and a space), plus an additional number of
+                    #   spaces matching the number of spaces that would be used in the
+                    #   tree_prefix of any *child* of this submodule.
+                    # - total_indent: This is the total indent needed to achieve the
+                    #   second goal. The first addition of 4 aligns the output with the
+                    #   status (e.g., "at tag ..."), accounting for the 3 leading
+                    #   characters before the name and the 1 trailing space after the
+                    #   name. The second addition of 4 indents the details about local
+                    #   mods an additional 4 spaces.
+                    # - trailing_spaces: This gives the correct total indentation given
+                    #   that we already have some leading spaces plus a vertical bar
+                    #   character.
+                    leading_spaces = " " * (3 + depth * tree_prefix_spaces)
+                    total_indent = full_width + 4 + 4
+                    trailing_spaces = " " * (total_indent - len(leading_spaces) - 1)
+                    result = (
+                        result
+                        + "\n"
+                        + textwrap.indent(
+                            status_output,
+                            leading_spaces + "│" + trailing_spaces,
+                            # The following predicate
+                            # makes the vertical bar
+                            # appear even for blank
+                            # lines:
+                            predicate=lambda _: True,
+                        )
+                    )
 
+        #        print(f"result {result} needsupdate {needsupdate} localmods {localmods} testfails {testfails}")
+        return result, needsupdate, localmods, testfails
 
     def _add_remote(self, git):
         """
@@ -171,11 +264,10 @@ def _add_remote(self, git):
         Returns:
             str: The name of the new remote if added, or the name of the existing remote that matches the submodule's URL.
         """
-        status, remotes = git.git_operation("remote", "-v")
+        _, remotes = git.git_operation("remote", "-v")
         remotes = remotes.splitlines()
-        upstream = None
+
         if remotes:
-            status, upstream = git.git_operation("ls-remote", "--get-url")
             newremote = "newremote.00"
             tmpurl = self.url.replace("git@github.com:", "https://github.com/")
             line = next((s for s in remotes if self.url in s or tmpurl in s), None)
@@ -215,7 +307,9 @@ def sparse_checkout(self):
         """
         self.logger.info("Called sparse_checkout for {}".format(self.name))
         rgit = GitInterface(self.root_dir, self.logger)
-        status, superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree")
+        status, superroot = rgit.git_operation(
+            "rev-parse", "--show-superproject-working-tree"
+        )
         if superroot:
             gitroot = superroot.strip()
         else:
@@ -226,7 +320,7 @@ def sparse_checkout(self):
             with open(rootdotgit) as f:
                 line = f.readline().rstrip()
                 if line.startswith("gitdir: "):
-                    rootdotgit = os.path.abspath(os.path.join(self.root_dir,line[8:]))
+                    rootdotgit = os.path.abspath(os.path.join(self.root_dir, line[8:]))
         assert os.path.isdir(rootdotgit)
         # first create the module directory
         if not os.path.isdir(os.path.join(self.root_dir, self.path)):
@@ -240,7 +334,9 @@ def sparse_checkout(self):
                 self.logger.info("Submodule {} found".format(self.name))
                 chk = sprepo_git.config_get_value("core", "sparseCheckout")
                 if chk == "true":
-                    self.logger.info("Sparse submodule {} already checked out".format(self.name))
+                    self.logger.info(
+                        "Sparse submodule {} already checked out".format(self.name)
+                    )
                     return
             except (NoOptionError):
                 self.logger.debug("Sparse submodule {} not present".format(self.name))
@@ -251,14 +347,16 @@ def sparse_checkout(self):
 
         # set the repository remote
 
-        self.logger.info("Setting remote origin in {}/{}".format(self.root_dir, self.path))
+        self.logger.info(
+            "Setting remote origin in {}/{}".format(self.root_dir, self.path)
+        )
         status, remotes = sprepo_git.git_operation("remote", "-v")
         if self.url not in remotes:
             sprepo_git.git_operation("remote", "add", "origin", self.url)
 
-        topgit = os.path.join(gitroot, ".git")
-
-        if gitroot != self.root_dir and os.path.isfile(os.path.join(self.root_dir, ".git")):
+        if gitroot != self.root_dir and os.path.isfile(
+            os.path.join(self.root_dir, ".git")
+        ):
             with open(os.path.join(self.root_dir, ".git")) as f:
                 gitpath = os.path.relpath(
                     os.path.join(self.root_dir, f.read().split()[1]),
@@ -273,8 +371,8 @@ def sparse_checkout(self):
 
         if os.path.isdir(os.path.join(self.root_dir, self.path, ".git")):
             with utils.pushd(sprep_repo):
-                if os.path.isdir(os.path.join(rootdotgit,".git")):
-                    shutil.rmtree(os.path.join(rootdotgit,".git"))
+                if os.path.isdir(os.path.join(rootdotgit, ".git")):
+                    shutil.rmtree(os.path.join(rootdotgit, ".git"))
                 shutil.move(".git", rootdotgit)
                 with open(".git", "w") as f:
                     f.write("gitdir: " + os.path.relpath(rootdotgit))
@@ -284,7 +382,9 @@ def sparse_checkout(self):
                 gitsparse = os.path.abspath(os.path.join(infodir, "sparse-checkout"))
                 if os.path.isfile(gitsparse):
                     self.logger.warning(
-                        "submodule {} is already initialized {}".format(self.name, rootdotgit)
+                        "submodule {} is already initialized {}".format(
+                            self.name, rootdotgit
+                        )
                     )
                     os.remove(gitsparse)
 
@@ -292,26 +392,28 @@ def sparse_checkout(self):
                     shutil.copy(self.fxsparse, gitsparse)
                 else:
                     self.logger.warning(
-                        "submodule {} could not find {}".format(self.name, self.fxsparse)
+                        "submodule {} could not find {}".format(
+                            self.name, self.fxsparse
+                        )
                     )
 
         # Finally checkout the repo
         sprepo_git.git_operation("fetch", "origin", "--tags")
-        status,_ = sprepo_git.git_operation("checkout", self.fxtag)
+        status, _ = sprepo_git.git_operation("checkout", self.fxtag)
         if status:
             print(f"Error checking out {self.name:>20} at {self.fxtag}")
         else:
             print(f"Successfully checked out {self.name:>20} at {self.fxtag}")
-        status,f = sprepo_git.git_operation("status")
+        status, f = sprepo_git.git_operation("status")
         # Restore any files deleted from sandbox
         for line in f.splitlines():
             if "deleted:" in line:
                 deleted_file = line.split("deleted:")[1].strip()
                 sprepo_git.git_operation("checkout", deleted_file)
 
-        rgit.config_set_value('submodule.' + self.name, "active", "true")
-        rgit.config_set_value('submodule.' + self.name, "url", self.url)
-        rgit.config_set_value('submodule.' + self.name, "path", self.path)
+        rgit.config_set_value("submodule." + self.name, "active", "true")
+        rgit.config_set_value("submodule." + self.name, "url", self.url)
+        rgit.config_set_value("submodule." + self.name, "path", self.path)
 
     async def update(self):
         """
@@ -337,7 +439,9 @@ async def update(self):
         """
         git = GitInterface(self.root_dir, self.logger)
         repodir = os.path.join(self.root_dir, self.path)
-        self.logger.info("Checkout {} into {}/{}".format(self.name, self.root_dir, self.path))
+        self.logger.info(
+            "Checkout {} into {}/{}".format(self.name, self.root_dir, self.path)
+        )
         # if url is provided update to the new url
         tag = None
         repo_exists = False
@@ -348,7 +452,9 @@ async def update(self):
         if self.fxsparse:
             print(f"Sparse checkout {self.name} fxsparse {self.fxsparse}")
             if not os.path.isfile(self.fxsparse):
-                self.logger.info("Submodule {} fxsparse file not found".format(self.name))
+                self.logger.info(
+                    "Submodule {} fxsparse file not found".format(self.name)
+                )
 
             self.sparse_checkout()
         else:
@@ -361,7 +467,9 @@ async def update(self):
                     git.git_operation("clone", self.url, self.path)
                     smgit = GitInterface(repodir, self.logger)
                     if not tag:
-                        status, tag = smgit.git_operation("describe", "--tags", "--always")
+                        status, tag = smgit.git_operation(
+                            "describe", "--tags", "--always"
+                        )
                     smgit.git_operation("checkout", tag)
                     # Now need to move the .git dir to the submodule location
                     rootdotgit = os.path.join(self.root_dir, ".git")
@@ -371,7 +479,9 @@ async def update(self):
                             if line.startswith("gitdir: "):
                                 rootdotgit = line[8:]
 
-                    newpath = os.path.abspath(os.path.join(self.root_dir, rootdotgit, "modules", self.name))
+                    newpath = os.path.abspath(
+                        os.path.join(self.root_dir, rootdotgit, "modules", self.name)
+                    )
                     if os.path.exists(newpath):
                         shutil.rmtree(os.path.join(repodir, ".git"))
                     else:
@@ -384,7 +494,9 @@ async def update(self):
                 parent = os.path.dirname(repodir)
                 if not os.path.isdir(parent):
                     os.makedirs(parent)
-                git.git_operation("submodule", "add", "--name", self.name, "--", self.url, self.path)
+                git.git_operation(
+                    "submodule", "add", "--name", self.name, "--", self.url, self.path
+                )
 
             if not repo_exists:
                 git.git_operation("submodule", "init", "--", self.path)
@@ -394,17 +506,17 @@ async def update(self):
                 smgit = GitInterface(repodir, self.logger)
                 newremote = self._add_remote(smgit)
                 # Trying to distingush a tag from a hash
-                allowed = set(string.digits + 'abcdef')
+                allowed = set(string.digits + "abcdef")
                 status = 0
                 if not set(self.fxtag) <= allowed:
                     # This is a tag
                     tag = f"refs/tags/{self.fxtag}:refs/tags/{self.fxtag}"
-                    status,_ = smgit.git_operation("fetch", newremote, tag)
+                    status, _ = smgit.git_operation("fetch", newremote, tag)
                 else:
                     # This is likely a hash, so fetch full history just in case
-                    status,_ = smgit.git_operation("fetch", newremote)
+                    status, _ = smgit.git_operation("fetch", newremote)
                 if status == 0:
-                    status,_ = smgit.git_operation("checkout", self.fxtag)
+                    status, _ = smgit.git_operation("checkout", self.fxtag)
                 if status:
                     utils.fatal_error(
                         f"Failed to checkout {self.name} at tag or hash {self.fxtag} from {repodir}"
@@ -415,7 +527,6 @@ async def update(self):
                     f"Failed to checkout {self.name} {repo_exists} {repodir} {self.path}"
                 )
 
-
         if os.path.exists(os.path.join(self.path, ".git")):
             submoddir = os.path.join(self.root_dir, self.path)
             with utils.pushd(submoddir):
@@ -431,10 +542,11 @@ async def update(self):
                 modfiles = []
                 moddirs = []
                 if files:
-                    for f in files.split('\0'):
+                    for f in files.split("\0"):
                         if f:
                             if os.path.exists(f):
-                                git.git_operation("checkout",f)
+                                self.logger.info(f"File {f} locally modified")
+                                modfiles.append(f)
                             elif os.path.isdir(f):
                                 moddirs.append(f)
                             else:
@@ -447,7 +559,6 @@ async def update(self):
                     except Exception as error:
                         print(error)
 
-
                 elif not fxtag:
                     print(f"No fxtag found for submodule {self.name:>20}")
                 elif modfiles:
@@ -457,6 +568,4 @@ async def update(self):
                 else:
                     print(f"{self.name:>20} up to date.")
 
-
-
         return
diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
index c4f43d5238..57752143f8 100644
--- a/.lib/git-fleximod/git_fleximod/utils.py
+++ b/.lib/git-fleximod/git_fleximod/utils.py
@@ -57,7 +57,16 @@ def printlog(msg, **kwargs):
 
 
 def find_upwards(root_dir, filename):
-    """Find a file in root dir or any of it's parents"""
+    """
+    Find a file in root dir or any of its parents.
+
+    >>> import tempfile, os
+    >>> with tempfile.TemporaryDirectory() as tmp:
+    ...     f = os.path.join(tmp, 'testfile.txt')
+    ...     open(f, 'w').close()
+    ...     find_upwards(tmp, 'testfile.txt').name == 'testfile.txt'
+    True
+    """
     d = Path(root_dir)
     root = Path(d.root)
     while d != root:
@@ -69,18 +78,8 @@ def find_upwards(root_dir, filename):
 
 
 def last_n_lines(the_string, n_lines, truncation_message=None):
-    """Returns the last n lines of the given string
-
-    Args:
-        the_string: str
-        n_lines: int
-        truncation_message: str, optional
-
-    Returns a string containing the last n lines of the_string
-
-    If truncation_message is provided, the returned string begins with
-    the given message if and only if the string is greater than n lines
-    to begin with.
+    """
+    Returns the last n lines of the given string.
     """
 
     lines = the_string.splitlines(True)
@@ -97,18 +96,12 @@ def last_n_lines(the_string, n_lines, truncation_message=None):
 
 
 def indent_string(the_string, indent_level):
-    """Indents the given string by a given number of spaces
-
-    Args:
-       the_string: str
-       indent_level: int
-
-    Returns a new string that is the same as the_string, except that
-    each line is indented by 'indent_level' spaces.
-
-    In python3, this can be done with textwrap.indent.
     """
+    Indents the given string by a given number of spaces.
 
+    >>> indent_string('a\\nb', 2)
+    '  a\\n  b'
+    """
     lines = the_string.splitlines(True)
     padding = " " * indent_level
     lines_indented = [padding + line for line in lines]
@@ -307,9 +300,8 @@ def execute_subprocess(commands, status_to_caller=False, output_to_caller=False)
         # simple status check. If returning, it is the callers
         # responsibility determine if an error occurred and handle it
         # appropriately.
-        msg_context = (
-            "Process did not run successfully; "
-            "returned status {0}".format(error.returncode)
+        msg_context = "Process did not run successfully; " "returned status {0}".format(
+            error.returncode
         )
         msg = failed_command_msg(msg_context, commands, output=error.output)
         if not return_to_caller:
diff --git a/.lib/git-fleximod/poetry.lock b/.lib/git-fleximod/poetry.lock
index ac82fb0d97..6c6af17b37 100644
--- a/.lib/git-fleximod/poetry.lock
+++ b/.lib/git-fleximod/poetry.lock
@@ -1,141 +1,177 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
 [[package]]
 name = "babel"
-version = "2.15.0"
+version = "2.17.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
-    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
-    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+    {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
+    {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
 ]
 
-[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
-
 [package.extras]
-dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata ; sys_platform == \"win32\""]
 
 [[package]]
 name = "certifi"
-version = "2024.8.30"
+version = "2025.11.12"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+groups = ["main"]
+files = [
+    {file = "certifi-2025.11.12-py3-none-any.whl", hash = "sha256:97de8790030bbd5c2d96b7ec782fc2f7820ef8dba6db909ccf95449f2d062d4b"},
+    {file = "certifi-2025.11.12.tar.gz", hash = "sha256:d8ab5478f2ecd78af242878415affce761ca6bc54a22a27e026d7c25357c3316"},
+]
+
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+description = "Validate configuration and produce human readable error messages."
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
 files = [
-    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
-    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.4"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
-python-versions = ">=3.7.0"
-files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
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+    {file = "charset_normalizer-3.4.4.tar.gz", hash = "sha256:94537985111c35f28720e43603b8e7b43a6ecfb2ce1d3058bbe955b73404e21a"},
 ]
 
 [[package]]
@@ -144,17 +180,32 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["main"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "distlib"
+version = "0.4.0"
+description = "Distribution utilities"
+optional = false
+python-versions = "*"
+groups = ["main"]
+files = [
+    {file = "distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16"},
+    {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"},
+]
+
 [[package]]
 name = "docutils"
 version = "0.19"
 description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "docutils-0.19-py3-none-any.whl", hash = "sha256:5e1de4d849fee02c63b040a4a3fd567f4ab104defd8a5511fbbc24a8a017efbc"},
     {file = "docutils-0.19.tar.gz", hash = "sha256:33995a6753c30b7f577febfc2c50411fec6aac7f7ffeb7c4cfe5991072dcf9e6"},
@@ -162,24 +213,42 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.3.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
-    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
-    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
+    {file = "exceptiongroup-1.3.1-py3-none-any.whl", hash = "sha256:a7a39a3bd276781e98394987d3a5701d0c4edffb633bb7a5144577f82c773598"},
+    {file = "exceptiongroup-1.3.1.tar.gz", hash = "sha256:8b412432c6055b0b7d14c310000ae93352ed6754f70fa8f7c34141f91c4e3219"},
 ]
 
+[package.dependencies]
+typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.13\""}
+
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "filelock"
+version = "3.19.1"
+description = "A platform independent file lock."
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "filelock-3.19.1-py3-none-any.whl", hash = "sha256:d38e30481def20772f5baf097c122c3babc4fcdb7e14e57049eb9d88c6dc017d"},
+    {file = "filelock-3.19.1.tar.gz", hash = "sha256:66eda1888b0171c998b35be2bcc0f6d75c388a7ce20c3f3f37aa8e96c2dddf58"},
+]
+
 [[package]]
 name = "fsspec"
 version = "2023.12.2"
 description = "File-system specification"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "fsspec-2023.12.2-py3-none-any.whl", hash = "sha256:d800d87f72189a745fa3d6b033b9dc4a34ad069f60ca60b943a63599f5501960"},
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@@ -211,13 +280,14 @@ tqdm = ["tqdm"]
 
 [[package]]
 name = "gitdb"
-version = "4.0.11"
+version = "4.0.12"
 description = "Git Object Database"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
-    {file = "gitdb-4.0.11-py3-none-any.whl", hash = "sha256:81a3407ddd2ee8df444cbacea00e2d038e40150acfa3001696fe0dcf1d3adfa4"},
-    {file = "gitdb-4.0.11.tar.gz", hash = "sha256:bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b"},
+    {file = "gitdb-4.0.12-py3-none-any.whl", hash = "sha256:67073e15955400952c6565cc3e707c554a4eea2e428946f7a4c162fab9bd9bcf"},
+    {file = "gitdb-4.0.12.tar.gz", hash = "sha256:5ef71f855d191a3326fcfbc0d5da835f26b13fbcba60c32c21091c349ffdb571"},
 ]
 
 [package.dependencies]
@@ -225,39 +295,61 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.43"
+version = "3.1.45"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
-    {file = "GitPython-3.1.43-py3-none-any.whl", hash = "sha256:eec7ec56b92aad751f9912a73404bc02ba212a23adb2c7098ee668417051a1ff"},
-    {file = "GitPython-3.1.43.tar.gz", hash = "sha256:35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c"},
+    {file = "gitpython-3.1.45-py3-none-any.whl", hash = "sha256:8908cb2e02fb3b93b7eb0f2827125cb699869470432cc885f019b8fd0fccff77"},
+    {file = "gitpython-3.1.45.tar.gz", hash = "sha256:85b0ee964ceddf211c41b9f27a49086010a190fd8132a24e21f362a4b36a791c"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
+typing-extensions = {version = ">=3.10.0.2", markers = "python_version < \"3.10\""}
+
+[package.extras]
+doc = ["sphinx (>=7.1.2,<7.2)", "sphinx-autodoc-typehints", "sphinx_rtd_theme"]
+test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock ; python_version < \"3.8\"", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions ; python_version < \"3.11\""]
+
+[[package]]
+name = "identify"
+version = "2.6.15"
+description = "File identification library for Python"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "identify-2.6.15-py2.py3-none-any.whl", hash = "sha256:1181ef7608e00704db228516541eb83a88a9f94433a8c80bb9b5bd54b1d81757"},
+    {file = "identify-2.6.15.tar.gz", hash = "sha256:e4f4864b96c6557ef2a1e1c951771838f4edc9df3a72ec7118b338801b11c7bf"},
+]
 
 [package.extras]
-doc = ["sphinx (==4.3.2)", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "sphinxcontrib-applehelp (>=1.0.2,<=1.0.4)", "sphinxcontrib-devhelp (==1.0.2)", "sphinxcontrib-htmlhelp (>=2.0.0,<=2.0.1)", "sphinxcontrib-qthelp (==1.0.3)", "sphinxcontrib-serializinghtml (==1.1.5)"]
-test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions"]
+license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.11"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
+groups = ["main"]
 files = [
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-    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
+    {file = "idna-3.11-py3-none-any.whl", hash = "sha256:771a87f49d9defaf64091e6e6fe9c18d4833f140bd19464795bc32d966ca37ea"},
+    {file = "idna-3.11.tar.gz", hash = "sha256:795dafcc9c04ed0c1fb032c2aa73654d8e8c5023a7df64a53f39190ada629902"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["main"]
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -265,43 +357,51 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.7.0"
 description = "Read metadata from Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "python_version == \"3.9\""
 files = [
-    {file = "importlib_metadata-8.0.0-py3-none-any.whl", hash = "sha256:15584cf2b1bf449d98ff8a6ff1abef57bf20f3ac6454f431736cd3e660921b2f"},
-    {file = "importlib_metadata-8.0.0.tar.gz", hash = "sha256:188bd24e4c346d3f0a933f275c2fec67050326a856b9a359881d7c2a697e8812"},
+    {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"},
+    {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"},
 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
-version = "2.0.0"
+version = "2.1.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+groups = ["main"]
 files = [
-    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
-    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+    {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"},
+    {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"},
 ]
 
 [[package]]
 name = "jinja2"
-version = "3.1.4"
+version = "3.1.6"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
-    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
-    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
+    {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
+    {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"},
 ]
 
 [package.dependencies]
@@ -312,119 +412,201 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.5"
+version = "3.0.3"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
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+optional = false
+python-versions = ">=3.9"
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+
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+virtualenv = ">=20.10.0"
 
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+version = "2.19.2"
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 [package.extras]
@@ -432,51 +614,126 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
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+version = "8.4.2"
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-iniconfig = "*"
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+packaging = ">=20"
+pluggy = ">=1.5,<2"
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 [package.extras]
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+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "requests", "setuptools", "xmlschema"]
 
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 ]
 
 [[package]]
 name = "requests"
-version = "2.32.3"
+version = "2.32.5"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6"},
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 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<4"
+charset_normalizer = ">=2,<4"
 idna = ">=2.5,<4"
 urllib3 = ">=1.21.1,<3"
 
@@ -486,24 +743,26 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "smmap"
-version = "5.0.1"
+version = "5.0.2"
 description = "A pure Python implementation of a sliding window memory map manager"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
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 ]
 
 [[package]]
 name = "snowballstemmer"
-version = "2.2.0"
-description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+version = "3.0.1"
+description = "This package provides 32 stemmers for 30 languages generated from Snowball algorithms."
 optional = false
-python-versions = "*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*"
+groups = ["main"]
 files = [
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+    {file = "snowballstemmer-3.0.1.tar.gz", hash = "sha256:6d5eeeec8e9f84d4d56b847692bacf79bc2c8e90c7f80ca4444ff8b6f2e52895"},
 ]
 
 [[package]]
@@ -512,6 +771,7 @@ version = "5.3.0"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "Sphinx-5.3.0.tar.gz", hash = "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"},
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@@ -539,51 +799,57 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
 lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"]
-test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
+test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast ; python_version < \"3.8\""]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.4"
+version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
+    {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.2"
-description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+version = "2.0.0"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
+    {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.1"
+version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
-    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
-    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
 [[package]]
@@ -592,6 +858,7 @@ version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
 optional = false
 python-versions = ">=3.5"
+groups = ["main"]
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
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@@ -602,68 +869,151 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+version = "2.0.0"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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+    {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
+    {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+version = "2.0.0"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
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 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.3.0"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version < \"3.11\""
 files = [
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+]
+
+[package.extras]
+dev = ["pytest", "setuptools"]
+
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.23.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "python_version == \"3.9\""
 files = [
-    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
-    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+    {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"},
+    {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
-lock-version = "2.0"
-python-versions = "^3.8"
-content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d"
+lock-version = "2.1"
+python-versions = ">=3.9"
+content-hash = "dcaa958aee9992b081f43d3efb409a2d8ece8e151ecb99064b741d57a29a86de"
diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
index 211eac1dd6..1e63c773f1 100644
--- a/.lib/git-fleximod/pyproject.toml
+++ b/.lib/git-fleximod/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "1.0.3"
+version = "1.1.1"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <jedwards@ucar.edu>"]
 maintainers = ["Jim Edwards <jedwards@ucar.edu>"]
@@ -20,13 +20,15 @@ me2flexi = "git_fleximod.metoflexi:_main"
 fsspec = "fsspec.fuse:main"
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = ">=3.9"
 GitPython = "^3.1.0"
 sphinx = "^5.0.0"
 fsspec = "^2023.12.2"
 wheel = "^0.42.0"
 pytest = "^8.0.0"
 pyfakefs = "^5.3.5"
+pre-commit = "4.3.0"
+wrapt = ">=2.0.0"
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues"
@@ -39,4 +41,3 @@ markers = [
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
-
diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
index 20271f4de2..b93fc74541 100644
--- a/.lib/git-fleximod/tbump.toml
+++ b/.lib/git-fleximod/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "1.0.3"
+current = "1.1.1"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before
diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py
index 44d28e1788..9d359fe530 100644
--- a/.lib/git-fleximod/tests/conftest.py
+++ b/.lib/git-fleximod/tests/conftest.py
@@ -1,68 +1,77 @@
-import pytest 
+import pytest
 from git_fleximod.gitinterface import GitInterface
-import os
 import subprocess
 import logging
-from pathlib import Path
 
-@pytest.fixture(scope='session')
+
+@pytest.fixture(scope="session")
 def logger():
     logging.basicConfig(
-        level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()]
+        level=logging.INFO,
+        format="%(name)s - %(levelname)s - %(message)s",
+        handlers=[logging.StreamHandler()],
     )
-    logger = logging.getLogger(__name__)
-    return logger
-
-all_repos=[
-    {"subrepo_path": "modules/test",
-     "submodule_name": "test_submodule",
-     "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_submodule at tag MPIserial_2.4.0",
-     "status3" : "test_submodule at tag MPIserial_2.4.0",
-     "status4" : "test_submodule at tag MPIserial_2.4.0",
-     "gitmodules_content" : """
+    llogger = logging.getLogger(__name__)
+    return llogger
+
+
+all_repos = [
+    {
+        "subrepo_path": "modules/test",
+        "submodule_name": "test_submodule",
+        "status1": "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+        "status2": "test_submodule at tag MPIserial_2.4.0",
+        "status3": "test_submodule at tag MPIserial_2.4.0",
+        "status4": "test_submodule at tag MPIserial_2.4.0",
+        "gitmodules_content": """
     [submodule "test_submodule"]
     path = modules/test
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelRequired
-"""},
-    {"subrepo_path": "modules/test_optional",
-     "submodule_name": "test_optional",
-     "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
-     "status2" : "test_optional at tag MPIserial_2.4.0",
-     "status3" : "test_optional not checked out, out of sync at tag MPIserial_2.5.4, expected tag is MPIserial_2.4.0 (optional)",
-     "status4" : "test_optional at tag MPIserial_2.4.0",
-     "gitmodules_content": """
+""",
+    },
+    {
+        "subrepo_path": "modules/test_optional",
+        "submodule_name": "test_optional",
+        "status1": "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0",
+        "status2": "test_optional at tag MPIserial_2.4.0",
+        "status3": "test_optional not checked out, out of sync at tag MPIserial_2.5.4, expected tag is MPIserial_2.4.0 (optional)",
+        "status4": "test_optional at tag MPIserial_2.4.0",
+        "gitmodules_content": """
      [submodule "test_optional"]
     path = modules/test_optional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = MPIserial_2.4.0
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = ToplevelOptional
-"""},
-    {"subrepo_path": "modules/test_alwaysoptional",
-     "submodule_name": "test_alwaysoptional",
-     "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
-     "status2" : "test_alwaysoptional at hash e5cf35c",
-     "status3" : "out of sync at tag MPIserial_2.5.4, expected tag is e5cf35c",
-     "status4" : "test_alwaysoptional at hash e5cf35c",
-     "gitmodules_content": """
+""",
+    },
+    {
+        "subrepo_path": "modules/test_alwaysoptional",
+        "submodule_name": "test_alwaysoptional",
+        "status1": "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c",
+        "status2": "test_alwaysoptional at hash e5cf35c",
+        "status3": "out of sync at tag MPIserial_2.5.4, expected tag is e5cf35c",
+        "status4": "test_alwaysoptional at hash e5cf35c",
+        "gitmodules_content": """
     [submodule "test_alwaysoptional"]
     path = modules/test_alwaysoptional
     url = https://github.com/ESMCI/mpi-serial.git
     fxtag = e5cf35c
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysOptional
-"""},    
-    {"subrepo_path": "modules/test_sparse",
-     "submodule_name": "test_sparse",
-     "status1" : "test_sparse at tag MPIserial_2.5.0",
-     "status2" : "test_sparse at tag MPIserial_2.5.0",
-     "status3" : "test_sparse at tag MPIserial_2.5.0",
-     "status4" : "test_sparse at tag MPIserial_2.5.0",
-     "gitmodules_content": """
+""",
+    },
+    {
+        "subrepo_path": "modules/test_sparse",
+        "submodule_name": "test_sparse",
+        "status1": "test_sparse at tag MPIserial_2.5.0",
+        "status2": "test_sparse at tag MPIserial_2.5.0",
+        "status3": "test_sparse at tag MPIserial_2.5.0",
+        "status4": "test_sparse at tag MPIserial_2.5.0",
+        "gitmodules_content": """
     [submodule "test_sparse"]
     path = modules/test_sparse
     url = https://github.com/ESMCI/mpi-serial.git
@@ -70,22 +79,29 @@ def logger():
     fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git
     fxrequired = AlwaysRequired
     fxsparse = ../.sparse_file_list
-"""},
+""",
+    },
 ]
-@pytest.fixture(params=all_repos)
 
+
+@pytest.fixture(params=all_repos)
 def shared_repos(request):
-    return request.param
+    repo_data = request.param
+    return repo_data
+
 
 @pytest.fixture
 def get_all_repos():
     return all_repos
 
+
 def write_sparse_checkout_file(fp):
     sparse_content = """m4
 """
     fp.write_text(sparse_content)
 
+
+# pylint: disable=redefined-outer-name
 @pytest.fixture
 def test_repo(shared_repos, tmp_path, logger):
     subrepo_path = shared_repos["subrepo_path"]
@@ -100,16 +116,25 @@ def test_repo(shared_repos, tmp_path, logger):
         (test_dir / subrepo_path).mkdir()
         # Add the sparse checkout file
         write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list")
-        gitp.git_operation("add","modules/.sparse_file_list")
+        gitp.git_operation("add", "modules/.sparse_file_list")
     else:
         gitp = GitInterface(str(test_dir), logger)
-        gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path)
+        gitp.git_operation(
+            "submodule",
+            "add",
+            "--depth",
+            "1",
+            "--name",
+            submodule_name,
+            "https://github.com/ESMCI/mpi-serial.git",
+            subrepo_path,
+        )
         assert test_dir.joinpath(".gitmodules").is_file()
-        gitp.git_operation("add",subrepo_path)
-    gitp.git_operation("commit","-a","-m","\"add submod\"")
+        gitp.git_operation("add", subrepo_path)
+    gitp.git_operation("commit", "-a", "-m", '"add submod"')
     test_dir2 = tmp_path / "testrepo2"
-    gitp.git_operation("clone",test_dir,test_dir2)
-    return test_dir2    
+    gitp.git_operation("clone", test_dir, test_dir2)
+    return test_dir2
 
 
 @pytest.fixture
@@ -118,33 +143,45 @@ def complex_repo(tmp_path, logger):
     test_dir.mkdir()
     str_path = str(test_dir)
     gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation(
+        "remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2"
+    )
     gitp.git_operation("fetch", "origin")
     gitp.git_operation("checkout", "v0.0.1")
     return test_dir
 
+
 @pytest.fixture
 def complex_update(tmp_path, logger):
     test_dir = tmp_path / "testcomplex"
     test_dir.mkdir()
     str_path = str(test_dir)
     gitp = GitInterface(str_path, logger)
-    gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2")
+    gitp.git_operation(
+        "remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2"
+    )
     gitp.git_operation("fetch", "origin")
     gitp.git_operation("checkout", "v0.0.2")
-    
+
     return test_dir
-    
+
+
 @pytest.fixture
 def git_fleximod():
-    def _run_fleximod(path, args, input=None):
+    def _run_fleximod(path, args, user_input=None):
         cmd = ["git", "fleximod"] + args.split()
-        result = subprocess.run(cmd, cwd=path, input=input, 
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
-                                text=True)
+        result = subprocess.run(
+            cmd,
+            cwd=path,
+            input=user_input,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+            check=False,
+        )
         if result.returncode:
             print(result.stdout)
             print(result.stderr)
         return result
-    return _run_fleximod
 
+    return _run_fleximod
diff --git a/.lib/git-fleximod/tests/test_a_import.py b/.lib/git-fleximod/tests/test_a_import.py
index d5ca878de5..939f143642 100644
--- a/.lib/git-fleximod/tests/test_a_import.py
+++ b/.lib/git-fleximod/tests/test_a_import.py
@@ -4,5 +4,6 @@
 from git_fleximod.gitinterface import GitInterface
 from git_fleximod.gitmodules import GitModules
 
+
 def test_import():
     print("here")
diff --git a/.lib/git-fleximod/tests/test_b_update.py b/.lib/git-fleximod/tests/test_b_update.py
index 159f1cfae0..e19bbb3d8b 100644
--- a/.lib/git-fleximod/tests/test_b_update.py
+++ b/.lib/git-fleximod/tests/test_b_update.py
@@ -1,26 +1,103 @@
-import pytest
+# tests/test_b_update.py
+import time
 from pathlib import Path
-                
+
+
 def test_basic_checkout(git_fleximod, test_repo, shared_repos):
     # Prepare a simple .gitmodules
-    gm = shared_repos['gitmodules_content']
-    file_path = (test_repo / ".gitmodules")
+    gm = shared_repos["gitmodules_content"]
+    file_path = test_repo / ".gitmodules"
     repo_name = shared_repos["submodule_name"]
     repo_path = shared_repos["subrepo_path"]
 
     file_path.write_text(gm)
-    
+
     # Run the command
     result = git_fleximod(test_repo, f"update {repo_name}")
 
     # Assertions
-    assert result.returncode == 0 
-    assert Path(test_repo / repo_path).exists()   # Did the submodule directory get created?
+    assert result.returncode == 0
+    assert Path(
+        test_repo / repo_path
+    ).exists()  # Did the submodule directory get created?
     if "sparse" in repo_name:
-        assert Path(test_repo /  f"{repo_path}/m4").exists()   # Did the submodule sparse directory get created?
-        assert not Path(test_repo /  f"{repo_path}/README").exists()   # Did only the submodule sparse directory get created?
-    
-    status = git_fleximod(test_repo, f"status {repo_name}")
-        
-    assert shared_repos["status2"] in status.stdout
-        
+        assert Path(
+            test_repo / f"{repo_path}/m4"
+        ).exists()  # Did the submodule sparse directory get created?
+        assert not Path(
+            test_repo / f"{repo_path}/README"
+        ).exists()  # Did only the submodule sparse directory get created?
+
+
+def test_local_modification_scenarios(git_fleximod, test_repo, shared_repos):
+    """
+    Test three scenarios for local modifications:
+    1. Local mods, repo in sync: update leaves local mods alone.
+    2. Local mods, repo out-of-sync, no conflict: update brings repo up to date, local mods retained, message shown.
+    3. Local mods, repo out-of-sync, conflict: update fails with error.
+    """
+    repo_name = shared_repos["submodule_name"]
+    repo_path = shared_repos["subrepo_path"]
+    submodule_dir = test_repo / repo_path
+
+    # Ensure submodule is checked out and at intended tag
+    gm = shared_repos["gitmodules_content"]
+    (test_repo / ".gitmodules").write_text(gm)
+    result = git_fleximod(test_repo, f"update {repo_name}")
+    assert result.returncode == 0
+    assert submodule_dir.exists()
+    test_file = submodule_dir / "README"
+    if not test_file.exists():
+        # README must exist in the repository for this test. If not, skip this test.
+        return
+
+    # --- Scenario 1: Local mods, repo in sync ---
+    original_content = test_file.read_text()
+    local_mod_content = f"local modification {time.time()}\n"
+    test_file.write_text(original_content + local_mod_content)
+    result1 = git_fleximod(test_repo, f"update {repo_name}")
+    assert result1.returncode == 0
+    assert (
+        test_file.read_text() == original_content + local_mod_content
+    ), "Local modification was overwritten when repo was in sync!"
+
+    # --- Scenario 2: Local mods, repo out-of-sync, no conflict ---
+    # Simulate out-of-sync by checking out previous commit/tag in submodule
+    import subprocess
+
+    # Try to checkout previous commit (if possible)
+    log = (
+        subprocess.check_output(["git", "log", "--pretty=oneline"], cwd=submodule_dir)
+        .decode()
+        .splitlines()
+    )
+    if len(log) > 1:
+        prev_hash = log[1].split()[0]
+        subprocess.check_call(["git", "checkout", prev_hash], cwd=submodule_dir)
+        # Make a local mod that does not conflict
+        test_file.write_text(original_content + local_mod_content)
+        result2 = git_fleximod(test_repo, f"update {repo_name}")
+        assert result2.returncode == 0
+        # Should retain local mod and show message
+        assert (
+            test_file.read_text() == original_content + local_mod_content
+        ), "Local modification was lost after update with no conflict!"
+        status = git_fleximod(test_repo, f"status {repo_name}")
+        assert "modified files" in status.stdout or "modified" in status.stdout.lower()
+
+    # --- Scenario 3: Local mods, repo out-of-sync, conflict ---
+    # Simulate conflict by modifying file and checking out previous commit that changes the same file
+    if len(log) > 2:
+        # Recover original README file
+        subprocess.check_call(["git", "restore", "README"], cwd=submodule_dir)
+        # Reset to a further previous commit\
+        conflict_hash = log[2].split()[0]
+        subprocess.check_call(["git", "checkout", conflict_hash], cwd=submodule_dir)
+        # Overwrite file with conflicting content
+        test_file.write_text("conflicting local mod\n")
+        try:
+            git_fleximod(test_repo, f"update {repo_name}")
+        except Exception as e:
+            assert "ERROR" in str(e) or "Failed to checkout" in str(
+                e
+            ), "Expected error not raised for conflict scenario!"
diff --git a/.lib/git-fleximod/tests/test_c_required.py b/.lib/git-fleximod/tests/test_c_required.py
index 2ac6614519..dd3dcf4f09 100644
--- a/.lib/git-fleximod/tests/test_c_required.py
+++ b/.lib/git-fleximod/tests/test_c_required.py
@@ -1,9 +1,11 @@
-import pytest
+# tests/test_c_required.py
 import re
-from pathlib import Path
-                
+
+from tests.utils_for_tests import normalize_whitespace
+
+
 def test_required(git_fleximod, test_repo, shared_repos):
-    file_path = (test_repo / ".gitmodules")
+    file_path = test_repo / ".gitmodules"
     gm = shared_repos["gitmodules_content"]
     repo_name = shared_repos["submodule_name"]
     if file_path.exists():
@@ -11,7 +13,7 @@ def test_required(git_fleximod, test_repo, shared_repos):
             gitmodules_content = f.read()
             # add the entry if it does not exist
             if repo_name not in gitmodules_content:
-                file_path.write_text(gitmodules_content+gm)
+                file_path.write_text(gitmodules_content + gm)
             # or if it is incomplete
             elif gm not in gitmodules_content:
                 file_path.write_text(gm)
@@ -20,15 +22,15 @@ def test_required(git_fleximod, test_repo, shared_repos):
     result = git_fleximod(test_repo, "update")
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status3"] in status.stdout
-    status = git_fleximod(test_repo, f"update --optional")
+    assert shared_repos["status3"] in normalize_whitespace(status.stdout)
+    status = git_fleximod(test_repo, "update --optional")
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
+    assert shared_repos["status4"] in normalize_whitespace(status.stdout)
     status = git_fleximod(test_repo, f"update {repo_name}")
     assert result.returncode == 0
     status = git_fleximod(test_repo, f"status {repo_name}")
-    assert shared_repos["status4"] in status.stdout
+    assert shared_repos["status4"] in normalize_whitespace(status.stdout)
 
     text = file_path.read_text()
     new_value = "somethingelse"
@@ -40,4 +42,8 @@ def test_required(git_fleximod, test_repo, shared_repos):
     file_path.write_text(new_text)
 
     result = git_fleximod(test_repo, f"update {repo_name}")
-    assert f'fatal: couldn\'t find remote ref' in result.stderr or 'error: pathspec \'somethingelse\' did not match any file(s) known to git' in result.stderr
+    assert (
+        "fatal: couldn't find remote ref" in result.stderr
+        or "error: pathspec 'somethingelse' did not match any file(s) known to git"
+        in result.stderr
+    )
diff --git a/.lib/git-fleximod/tests/test_d_complex.py b/.lib/git-fleximod/tests/test_d_complex.py
index edde7d816d..f7cb9c92fe 100644
--- a/.lib/git-fleximod/tests/test_d_complex.py
+++ b/.lib/git-fleximod/tests/test_d_complex.py
@@ -1,34 +1,57 @@
-import pytest
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
+# tests/test_d_complex.py
+
+from tests.utils_for_tests import normalize_whitespace
+
 
 def test_complex_checkout(git_fleximod, complex_repo, logger):
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, aligned at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
-    
+    logger.debug("test_complex_checkout status:\n" + status.stdout)
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert "Complex not checked out, aligned at tag testtag02" in normalize_whitespace(
+        status.stdout
+    )
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
+
     # This should checkout and update test_submodule and complex_sub
-    result = git_fleximod(complex_repo, "update")    
+    result = git_fleximod(complex_repo, "update")
     assert result.returncode == 0
 
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag02" in normalize_whitespace(status.stdout)
 
     # now check the complex_sub
-    root = (complex_repo / "modules" / "complex")
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+    root = complex_repo / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serial" / ".git").exists()
+    assert not (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
 
     # update a single optional submodule
 
@@ -36,31 +59,42 @@ def test_complex_checkout(git_fleximod, complex_repo, logger):
     assert result.returncode == 0
 
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag02" in normalize_whitespace(status.stdout)
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
 
     # Finally update optional
     result = git_fleximod(complex_repo, "update --optional")
     assert result.returncode == 0
 
     status = git_fleximod(complex_repo, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag02" in status.stdout)
-    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
-    
-    # now check the complex_sub
-    root = (complex_repo / "modules" / "complex" )
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag02" in normalize_whitespace(status.stdout)
+    assert "AlwaysOptional at tag MPIserial_2.3.0" in normalize_whitespace(
+        status.stdout
+    )
 
+    # now check the complex_sub
+    root = complex_repo / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
diff --git a/.lib/git-fleximod/tests/test_e_complex_update.py b/.lib/git-fleximod/tests/test_e_complex_update.py
index 0c3ab4c6a6..b529a64788 100644
--- a/.lib/git-fleximod/tests/test_e_complex_update.py
+++ b/.lib/git-fleximod/tests/test_e_complex_update.py
@@ -1,35 +1,58 @@
-import pytest
-from pathlib import Path
-from git_fleximod.gitinterface import GitInterface
+# tests/test_e_complex_update.py
+from tests.utils_for_tests import normalize_whitespace
+
 
 def test_complex_update(git_fleximod, complex_update, logger):
+    logger.debug("Starting test_complex_update")
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex not checked out, out of sync at tag testtag02, expected tag is testtag3" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
-    
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "Complex not checked out, out of sync at tag testtag02, expected tag is testtag3"
+        in normalize_whitespace(status.stdout)
+    )
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
+
     # This should checkout and update test_submodule and complex_sub
-    result = git_fleximod(complex_update, "update")    
+    result = git_fleximod(complex_update, "update")
     assert result.returncode == 0
 
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag3" in status.stdout)
+    assert (
+        "ToplevelOptional not checked out, aligned at tag v5.3.2"
+        in normalize_whitespace(status.stdout)
+    )
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag3" in normalize_whitespace(status.stdout)
 
     # now check the complex_sub
-    root = (complex_update / "modules" / "complex")
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serialAR" / ".git").exists())
-    assert((root / "modules" / "mpi-serialSAR" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
+    root = complex_update / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serialAR" / ".git").exists()
+    assert (root / "modules" / "mpi-serialSAR" / ".git").exists()
+    assert not (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
 
     # update a single optional submodule
 
@@ -37,33 +60,44 @@ def test_complex_update(git_fleximod, complex_update, logger):
     assert result.returncode == 0
 
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag3" in status.stdout)
-    assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout)
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag3" in normalize_whitespace(status.stdout)
+    assert (
+        "AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0"
+        in normalize_whitespace(status.stdout)
+    )
 
     # Finally update optional
     result = git_fleximod(complex_update, "update --optional")
     assert result.returncode == 0
 
     status = git_fleximod(complex_update, "status")
-    assert("ToplevelOptional at tag v5.3.2" in status.stdout)
-    assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout)
-    assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout)
-    assert("Complex at tag testtag3" in status.stdout)
-    assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout)
-    
-    # now check the complex_sub
-    root = (complex_update / "modules" / "complex" )
-    assert(not (root / "libraries" / "gptl" / ".git").exists())
-    assert(not (root / "libraries" / "mpi-serial" / ".git").exists())
-    assert(not (root / "modules" / "mpi-serial" / ".git").exists())
-    assert((root / "modules" / "mpi-serialAR" / ".git").exists())
-    assert((root / "modules" / "mpi-serialSAR" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / ".git").exists())
-    assert((root / "modules" / "mpi-serial2" / ".git").exists())
-    assert((root / "modules" / "mpi-sparse" / "m4").exists())
-    assert(not (root / "modules" / "mpi-sparse" / "README").exists())
-
+    assert "ToplevelOptional at tag v5.3.2" in normalize_whitespace(status.stdout)
+    assert "ToplevelRequired at tag MPIserial_2.5.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "AlwaysRequired at tag MPIserial_2.4.0" in normalize_whitespace(
+        status.stdout
+    )
+    assert "Complex at tag testtag3" in normalize_whitespace(status.stdout)
+    assert "AlwaysOptional at tag MPIserial_2.3.0" in normalize_whitespace(
+        status.stdout
+    )
 
+    # now check the complex_sub
+    root = complex_update / "modules" / "complex"
+    assert not (root / "libraries" / "gptl" / ".git").exists()
+    assert not (root / "libraries" / "mpi-serial" / ".git").exists()
+    assert not (root / "modules" / "mpi-serial" / ".git").exists()
+    assert (root / "modules" / "mpi-serialAR" / ".git").exists()
+    assert (root / "modules" / "mpi-serialSAR" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / ".git").exists()
+    assert (root / "modules" / "mpi-serial2" / ".git").exists()
+    assert (root / "modules" / "mpi-sparse" / "m4").exists()
+    assert not (root / "modules" / "mpi-sparse" / "README").exists()
diff --git a/.lib/git-fleximod/tests/utils_for_tests.py b/.lib/git-fleximod/tests/utils_for_tests.py
new file mode 100644
index 0000000000..8b6f57e2e8
--- /dev/null
+++ b/.lib/git-fleximod/tests/utils_for_tests.py
@@ -0,0 +1,13 @@
+"""
+Helper functions that can be used in tests
+"""
+
+
+def normalize_whitespace(text):
+    """
+    Normalize whitespace for flexible string comparisons in tests.
+
+    This removes leading and trailing whitespace and collapses other whitespace down to a
+    single space.
+    """
+    return " ".join(text.split())
diff --git a/ccs_config b/ccs_config
index 6c22a0f514..7fda4a54ec 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit 6c22a0f514cb8ab1d4bcf403b22109b561c42955
+Subproject commit 7fda4a54ec6261d2affb2351ca2b8f288308f0e8
diff --git a/cime b/cime
index cd1046c5c2..e2cf67742b 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit cd1046c5c2c5b74c6fbfc46058f6512caab1cf1f
+Subproject commit e2cf67742b1da605da1f782bb53e85915e375a3c
diff --git a/components/cdeps b/components/cdeps
index 293774652f..7e51a85aa2 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit 293774652f41d5daf5614135fc41b676e8bc59d8
+Subproject commit 7e51a85aa2f4a645ca6795ff63cd3eaa54e85453
diff --git a/components/cmeps b/components/cmeps
index 18eb93be8f..cbc1f0fd44 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 18eb93be8f80286739fbea7b500a069fb0d71aa8
+Subproject commit cbc1f0fd442066d171a973ad45d7f867f8cae6c6
diff --git a/components/mizuRoute b/components/mizuRoute
index 07dfd26a17..f4c3482f2b 160000
--- a/components/mizuRoute
+++ b/components/mizuRoute
@@ -1 +1 @@
-Subproject commit 07dfd26a17acb914b9036f59a8c6237990da09f2
+Subproject commit f4c3482f2b29b17ff66c00b615b3305c616fc85a
diff --git a/share b/share
index 14338bef3f..7e6d7a7854 160000
--- a/share
+++ b/share
@@ -1 +1 @@
-Subproject commit 14338bef3fa604d49160e376257264db1d3313e5
+Subproject commit 7e6d7a7854ccb8e80683d3dcc6e41220eef01896
diff --git a/tools/CUPiD b/tools/CUPiD
index 3d9531779b..880f3b3099 160000
--- a/tools/CUPiD
+++ b/tools/CUPiD
@@ -1 +1 @@
-Subproject commit 3d9531779b6f3e4c26059b10ba67c0f4477684e5
+Subproject commit 880f3b30997d19f1b766c483af957277866bbe74