Fix cancel allowlist regex and move methodology handler before git-clean

The cancel-rlcr-loop.sh allowlist in the bash validator matched when the
script name appeared as an argument to another command (e.g. cp). Anchor
the regex to the start of the command string so only direct invocations
are allowed.

Move the methodology analysis completion handler in the stop hook to run
before the git-clean check. Writing methodology artifacts can make the
working tree appear dirty when .humanize is tracked, which would block
exit before the handler ever ran.

Author: SihaoLiu

hooks/loop-bash-validator.sh

@@ -85,9 +85,9 @@ ACTIVE_PR_LOOP_DIR=$(find_active_pr_loop "$PR_LOOP_BASE_DIR")
 _MA_BASH_DIR="$ACTIVE_LOOP_DIR"
 
 if [[ -n "$_MA_BASH_DIR" ]] && [[ -f "$_MA_BASH_DIR/methodology-analysis-state.md" ]]; then
-    # Allow cancel-rlcr-loop.sh (user must be able to cancel during this phase)
-    # Only allow standalone invocation -- reject if chained with shell operators
-    if echo "$COMMAND_LOWER" | grep -qE '(^|[[:space:]])([^[:space:]]*/)?cancel-rlcr-loop\.sh' && \
+    # Allow cancel-rlcr-loop.sh only as the leading command (not as an argument
+    # to another command like cp/mv). Reject if chained with shell operators.
+    if echo "$COMMAND_LOWER" | grep -qE '^[[:space:]]*("?[^"]*/?)?cancel-rlcr-loop\.sh' && \
        ! echo "$COMMAND_LOWER" | grep -qE '[;|&]'; then
         exit 0
     fi

hooks/loop-codex-stop-hook.sh

@@ -582,6 +582,28 @@ Split these into smaller modules before continuing."
     fi
 fi
 
+# ========================================
+# Methodology Analysis Phase Completion Handler
+# ========================================
+# When in methodology analysis phase, check if the analysis is done.
+# If done, rename state to the original exit reason's terminal state.
+# If not done, block and ask Claude to complete the analysis.
+# All other checks (summary, bitlesson, goal tracker, max iterations) are skipped.
+# IMPORTANT: This MUST run before the git-clean check, because methodology
+# artifacts (.humanize/rlcr/...) may make the working tree appear dirty
+# if .humanize is tracked, which would block exit before reaching this handler.
+
+if [[ "$IS_METHODOLOGY_ANALYSIS_PHASE" == "true" ]]; then
+    if complete_methodology_analysis; then
+        # Analysis complete, allow exit
+        exit 0
+    else
+        # Analysis not yet complete, block
+        block_methodology_analysis_incomplete
+        exit 0
+    fi
+fi
+
 # ========================================
 # Quick Check: Git Clean and Pushed?
 # ========================================
@@ -682,25 +704,6 @@ Please push before exiting."
     fi
 fi
 
-# ========================================
-# Methodology Analysis Phase Completion Handler
-# ========================================
-# When in methodology analysis phase, check if the analysis is done.
-# If done, rename state to the original exit reason's terminal state.
-# If not done, block and ask Claude to complete the analysis.
-# All other checks (summary, bitlesson, goal tracker, max iterations) are skipped.
-
-if [[ "$IS_METHODOLOGY_ANALYSIS_PHASE" == "true" ]]; then
-    if complete_methodology_analysis; then
-        # Analysis complete, allow exit
-        exit 0
-    else
-        # Analysis not yet complete, block
-        block_methodology_analysis_incomplete
-        exit 0
-    fi
-fi
-
 # ========================================
 # Check Summary File Exists
 # ========================================