remove mentions of JEventProcessorSequentialRoot, deprecate external plugins (#1995)

### Briefly, what does this PR introduce?
JEventProcessorSequentialRoot was never used and removed in the latest
JANA2 release JeffersonLab/JANA2#456
Let's remove the references to it. Those come from unmaintained
documentation and deprecated benchmark, so my proposal is to remove
those pieces.

**This deprecates support for external plugins**.

### What kind of change does this PR introduce?
- [ ] Bug fix (issue #__)
- [ ] New feature (issue #__)
- [ ] Documentation update
- [ ] Other: __

### Please check if this PR fulfills the following:
- [ ] Tests for the changes have been added
- [ ] Documentation has been added / updated
- [ ] Changes have been communicated to collaborators

### Does this PR introduce breaking changes? What changes might users
need to make to their code?
No

### Does this PR change default behavior?
No

Author: veprbl

.github/workflows/linux-eic-shell.yml

@@ -549,45 +549,6 @@ jobs:
         path: two_stage_rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4eic.root
         if-no-files-found: error
 
-  eicrecon-eicmkplugin:
-    runs-on: ubuntu-24.04
-    needs:
-    - build
-    - npsim-gun
-    strategy:
-      matrix:
-        CXX: [g++]
-        particle: [e]
-        detector_config: [craterlake]
-    steps:
-    - name: Checkout .github
-      uses: actions/checkout@v4
-      with:
-        sparse-checkout: .github
-    - name: Download install directory
-      uses: actions/download-artifact@v4
-      with:
-        name: install-${{ matrix.CXX }}-eic-shell-Release-${{ env.platform }}-${{ env.release }}-ASAN
-    - name: Unarchive install directory
-      run: tar -xaf install.tar.zst
-    - uses: actions/download-artifact@v4
-      with:
-        name: sim_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4hep.root
-    - uses: cvmfs-contrib/github-action-cvmfs@v5
-    - name: Run EICrecon
-      uses: eic/run-cvmfs-osg-eic-shell@main
-      with:
-        platform-release: "${{ env.platform }}:${{ env.release }}"
-        setup: "/opt/detector/epic-${{ env.detector-version }}/bin/thisepic.sh"
-        run: |
-          export DETECTOR_CONFIG=${DETECTOR}_${{ matrix.detector_config }}
-          export LD_LIBRARY_PATH=$PWD/install/lib:$LD_LIBRARY_PATH
-          export JANA_PLUGIN_PATH=$PWD/install/lib/EICrecon/plugins${JANA_PLUGIN_PATH:+:${JANA_PLUGIN_PATH}}
-          $PWD/install/bin/eicmkplugin.py MyCustomPlugin
-          cmake -S MyCustomPlugin -B MyCustomPlugin/build -DEICrecon_ROOT=$PWD/install -DUSER_PLUGIN_OUTPUT_DIRECTORY=$PWD/install/lib/EICrecon/plugins
-          cmake --build MyCustomPlugin/build -j $(getconf _NPROCESSORS_ONLN) --target install
-          $PWD/install/bin/eicrecon ${{env.JANA_OPTIONS}} ${{env.JANA_OPTIONS_GUN}} -Pplugins=MyCustomPlugin -Ppodio:output_file=rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4eic.root sim_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4hep.root
-
   eicrecon-test-plugins:
     runs-on: ubuntu-24.04
     needs:
@@ -644,10 +605,8 @@ jobs:
         particle: [e]
         detector_config: [craterlake]
         benchmark_plugins:
-        - EcalBarrelScFiCheck
         - femc_studies
         - lfhcal_studies
-        - TRACKINGcheck
         - tracking_efficiency
         - tracking_occupancy
     steps:

docs/_sidebar.md

@@ -6,7 +6,6 @@
     * [Run DD4Hep simulation](howto/run_dd4hep_simulation.md)
     * [Use docker](howto/use_docker.md)
     * [Use singularity](howto/use_singularity.md)
-    * [Make Plugin](howto/make_plugin.md)
     * [Add Factory](howto/add_factory.md)
     * [Visualize Callgraph](howto/visualize_callgraph.md)
 * Design
@@ -23,9 +22,8 @@
 * Tutorials
     * [Introduction](tutorial/01-introduction.md)
     * [Work environment](tutorial/02-work-environment.md)
-    * [End user plugin](tutorial/03-end-user-plugin.md)
-    * [Factory](tutorial/04-factory.md)
-    * [Contributing](tutorial/05-contributing.md)
+    * [Factory](tutorial/03-factory.md)
+    * [Contributing](tutorial/04-contributing.md)
 * Misc
     * [References](misc/references.md)
 * Flags

docs/get-started/eic-shell.md

@@ -72,5 +72,4 @@ Example:
     eicrecon -Pplugins=plugin1,plugin2,plugin3 -Pnthreads=8 inputfile1.txt
 ~~~
 
-At this point, you can [create your own user plugin](/howto/make_plugin.md) or
-[add a new factory (i.e. algorithm)](/howto/add_factory.md).
+At this point, you can [add a new factory (i.e. algorithm)](/howto/add_factory.md).

docs/howto/add_factory.md

@@ -160,8 +160,7 @@ extern "C" {
 
 ## Testing the new factory
 
-Please follow the instructions on [creating a user plugin](HowTo_make_plugin.md)
-to get a working plugin. Then add these lines in the inidacted places:
+Add these lines in your plugin:
 
 ```cpp
 // Place this at the top of the processor header file (e.g. DaveTestProcessor.h)

docs/howto/make_plugin.md

@@ -10,7 +10,7 @@
 ## Introduction
 
 
-Now that you've learned about JANA plugins and JEventProcessors, let's talk about JFactories. JFactories are another essential JANA component just like JEventProcessors and JEventSources. While JEventProcessors are used for _aggregating_ results from each event into a structured output such as a histogram or a file, JFactories are used for computing those results in an organized way.
+Let's talk about JFactories. JFactories are another essential JANA component just like JEventProcessors and JEventSources. While JEventProcessors are used for _aggregating_ results from each event into a structured output such as a histogram or a file, JFactories are used for computing those results in an organized way.
 
 
 ### When do I use a JFactory?
@@ -31,14 +31,6 @@ Now that you've learned about JANA plugins and JEventProcessors, let's talk abou
 4. You can simply ask for the results you need and the JFactory will provide it. If nobody needs the results from the JFactory, it won't be run. If the results were already in the input file, it won't be run. If there are multiple consumers, the results are only computed once and then cached. If the JFactory relies on results from other JFactories, it will call them transparently and recursively.
 
 
-### When do I create my own plugin?
-
-- If you are doing a one-off prototype, it's fine to just use a ROOT macro.
-- If you are writing code you'll probably return to, we recommend putting the code in a standalone (i.e. outside of the EICrecon source tree) plugin.
-- If you are writing code other people will probably want to run, we recommend adding your plugin to the EICrecon source tree.
-- If you are writing a JFactory, we recommend adding it to the EICrecon source tree, either to an existing plugin or to a new one.
-
-
 ## Algorithms vs Factories
 
 In general, a Factory is a programming pattern for constructing objects in an abstract way. Oftentimes, the Factory is calling an algorithm under the hood.

docs/tutorial/03-end-user-plugin.md

@@ -1,5 +1,3 @@
-add_subdirectory(detectors/EcalBarrelScFiCheck)
-add_subdirectory(reconstruction/TRACKINGcheck)
 add_subdirectory(reconstruction/tracking_occupancy)
 add_subdirectory(reconstruction/tracking_efficiency)
 add_subdirectory(reconstruction/lfhcal_studies)