…cation

Wave 1 of the Maven merge plan (.sisyphus/plans/maven-merge.md):

T1: Pre-merge baseline build (./build-coatjava.sh -T4 --unittests
    --nomaps --nonets -Dmaven.test.failure.ignore=true)
    - coat-libs-13.8.4-SNAPSHOT.jar: 24210 classes captured
    - manifest: 5 entries (Implementation-Version=13.8.4-SNAPSHOT etc)
    - 33 services jars in install tree
    - 4 known pre-existing test failures (DC, EB, CVT reconstruction;
      AHDC pytorch loader): documented as baseline for T27 parity
T2: cnuphys/numRec orphan: DECISION = ABSORB-AS-SOURCE
    (in-tree sources 2025-11-17 are newer than 2014 external artifact)
T3: META-INF/services SPI: 0 entries, 0 collisions (no
    ServicesResourceTransformer needed in T9 shade plugin)
T4: Main resources: 294 files, 0 in-jar path collisions
T5: Test FQNs: 13 classes across 8 modules, 0 collisions
T6: coat-libs downstream consumers: 5 direct Maven deps in 3 repos
    (mon12, clas12calibration-dc, clas12alignment); 0 manifest readers
    found (-> T29 manifest parity bar is ADVISORY)
T7: Dependency analyzer audit: 4 mandatory new ignore entries
    (vectorgraphics2d, exp4j, jamapack, jMath); 3 optional for JavaFX
    classifier mismatch. Critical caveats: must preserve jevio
    classifier=jar-with-dependencies and pytorch-native-cpu
    classifier=linux-x86_64 when authoring T8 root pom.xml.

Refs: plan tasks T1-T7 (Wave 1)

build(merge): create unified root pom.xml (T8)

Replace 50-POM multi-module aggregator with a single-module root pom.xml:
- groupId/artifactId: org.jlab.coat:coatjava (per interview D6)
- packaging: jar (was pom)
- Removed <modules> block
- Added <distributionManagement> ported from reconstruction/coat-libs POMs
- Added union of all external <dependencies> from the 50 child POMs
  (internal coords filtered per .sisyphus/evidence/task-7 audit; numRec
  was ABSORB-AS-SOURCE per T2 so dropped; f2jutil kept as external)
- Preserved <dependencyManagement>, <repositories>, <properties>,
  enforcer/compiler/jar/jacoco/javadoc/spotbugs plugin config verbatim
- Ported reconstruction/alert/pom.xml copy-dependencies execution
  (copies ai.djl runtime jars into target/lib/services for runtime SPI)
- Preserved skip-tests profile (default-active)
- flatten-maven-plugin / maven-deploy-plugin remain in pluginManagement
  awaiting T10 wiring
- maven-shade-plugin NOT YET ported (T9 will)
- maven-dependency-plugin analyze-only ignoredUnusedDeclaredDependencies
  not yet expanded (T11 will, per T7 audit)

JavaFX deps carry classifier=linux to match the existing
<dependencyManagement> entries (else Maven rejects them as missing
version). T11 may revisit when running analyze-only end-to-end.

Validation:
  mvn -N validate => BUILD SUCCESS
  Effective POM written to .sisyphus/evidence/task-8/effective-pom.xml
  Only external cnuphys ref is cnuphys:f2jutil.

build(merge): port maven-shade-plugin execution to root POM (T9)

Adds shade-coat-libs execution at package phase that attaches a secondary
artifact (classifier=coat-libs) alongside the primary thin coatjava jar.

Adaptations from pre-merge common-tools/coat-libs/pom.xml:

  Artifact excludes:
  - DROPPED: cnuphys:cnuphys, cnuphys:jogl-all, cnuphys:jogl, cnuphys:gluegen
    Those classes are not reachable transitively in the current build:
    baseline coat-libs jar has 0 entries under com/jogamp, org/jogamp, or
    cnuphys/ced. The old excludes were defensive against historical
    transitive resolutions that no longer occur. Confirmed by
    .sisyphus/evidence/task-1-baseline/coat-libs-classes.txt.
  - KEPT: org.jlab.coda:jclara, org.jacoco
  - ADDED: ai.djl:*, ai.djl.pytorch:*
    Reason: ai.djl is declared in the merged root POM (was previously only
    in reconstruction/alert/pom.xml) so shade would now pull it into
    coat-libs unless excluded. The pre-merge baseline coat-libs has no
    ai/djl/* entries, and ai.djl jars are delivered to coatjava/lib/services/
    via maven-dependency-plugin copy-dependencies (added in T8).

  Filters (META-INF/*.SF/*.DSA/*.RSA, META-INF/maven/**, module-info.class,
  IDE files): ported verbatim (9 entries).

  ManifestResourceTransformer:
  - Specification-Title / Implementation-Title hard-coded to literal
    'coat-libs' (NOT ${project.artifactId} which is now 'coatjava'),
    preserving the pre-merge manifest contents byte-for-byte for T29.
  - Implementation-Vendor-Id = ${project.groupId} = 'org.jlab.coat'
    (matches pre-merge since coat-libs was already 'org.jlab.coat').
  - Specification-Version / Implementation-Version unchanged.

Secondary-artifact attach strategy (shadedArtifactAttached=true +
shadedClassifierName=coat-libs) produces target/coatjava-<v>-coat-libs.jar.
T20 (build-coatjava.sh) renames this to coat-libs-<v>.jar when installing
to coatjava/lib/clas/, and T24 (deploy-coatjava.sh) handles the deploy.

createDependencyReducedPom=false - flatten-maven-plugin (wired in T10) is
the authority on the published POM.

Validation:
  mvn -N validate => BUILD SUCCESS
  Full class-list parity check is T28 (after sources merged in T12-T18).

build(merge): activate flatten-maven-plugin under build/plugins (T10)

Moves flatten-maven-plugin and maven-deploy-plugin from <pluginManagement>
into <build><plugins> so they execute on this single-module project
(pluginManagement entries do nothing unless explicitly declared by a
plugin block, which made sense for the multi-module aggregator but not
for the merged jar project).

Flatten config:
- flattenMode=fatjar (matches pre-merge coat-libs)
- bound to package phase
- writes target/.flattened-pom.xml

maven-deploy-plugin config:
- pomFile=${project.build.directory}/.flattened-pom.xml
- deploy-coatjava.sh (T24) will use `mvn deploy:deploy-file
  -DpomFile=.flattened-pom.xml` when publishing the coat-libs uber-jar
  with its own GAV coordinates (org.jlab.coat:coat-libs:<version>).

pluginManagement block kept (empty) for future per-execution overrides.

Validation:
  mvn -N validate => BUILD SUCCESS
  Full flatten output verification deferred until T27 (after sources
  merged + first full package phase runs).

build(merge): expand ignoredUnusedDeclaredDependencies for merged scope (T11)

Per the T7 audit (.sisyphus/evidence/task-7/analyzer-audit.md), four
additional unused-declared ignores are required to prevent the
maven-dependency-plugin analyze-only execution from failing
`mvn verify` post-merge. These artifacts were declared in the pre-merge
common-tools/coat-libs/pom.xml (which had analyzer skipped) and now appear
as top-level deps of the merged project; they have zero compile imports
under src/main/java because they're shaded into coat-libs solely for
downstream consumers (mon12, iguana, clas12calibration-dc, clas12alignment):

  - de.erichseifert:vectorgraphics2d  (vector graphics export)
  - net.objecthunter:exp4j            (expression parser)
  - org.jama:jamapack                 (legacy Jampack/* linalg)
  - org.jlab.plugins:jMath            (legacy geometry/vector API)

JavaFX classifier mismatch (javafx-base/graphics/fxml :linux variant vs
bare coord) does NOT need ignore entries because T8 already declares
the deps with <classifier>linux</classifier> matching the
<dependencyManagement> entries.

Validation:
  mvn -N validate => BUILD SUCCESS
  Full analyzer run is part of T27 (needs compiled classes).

refactor(merge): git mv common-tools sources into src/main/java (T12)

Moves 628 tracked files from common-tools/<mod>/src/main/java/** into
src/main/java/** to consolidate the project under a single source tree.
Includes 619 .java files, 1 README.md, and 8 .java-BAK editor backups
(left tracked from upstream; relocated for history continuity).

Scope: common-tools modules except cnuphys/* (handled by T14).
Excluded: stale .swp editor swap file (untracked).

No file content changes; pure renames. History preserved via git mv.

Plan: .sisyphus/plans/maven-merge.md T12

refactor(merge): git mv common-tools resources into src/main/resources (T13)

Moves 294 tracked resource files from common-tools/<mod>/src/main/resources/**
into src/main/resources/**. Source modules: clara-io (9), clas-io (13),
clas-jcsg (268), clas-logging (3), coat-libs (1). Excludes cnuphys/* (T14).

No collisions (T4 inventory confirmed 0 in-jar path collisions). Pure
renames, no content changes.

Plan: .sisyphus/plans/maven-merge.md T13

refactor(merge): git mv cnuphys sources into src/main/java (T14)

Moves 539 .java files into src/main/java/**:
- magfield (46), snr (20), splot (116), swimmer (100) from cnuphys subs
  using standard src/main/java layout
- numRec (257) absorbed as source per T2 decision (ABSORB-AS-SOURCE),
  moving src/com/nr/** -> src/main/java/com/nr/**

Scope: java files only. 25 non-.java tracked files (build.xml, .gitignore
fragments) intentionally left behind in cnuphys sub directories; they are
Ant/legacy debris with no role in the merged Maven project and will be
removed by T19 (child-POM + empty-dir cleanup). Top-level build.xml
collision (magfield vs splot vs swimmer) is avoided by this exclusion.

numRec test/com/nr/test/** (308 files) remains for T17 (tests).

Pure renames, no content changes. History preserved.

Plan: .sisyphus/plans/maven-merge.md T14

refactor(merge): git mv reconstruction sources into src/main/java (T15)

Moves 408 tracked source files from reconstruction/<mod>/src/main/java/**
into src/main/java/**:
- 404 .java files across 26 modules (urwell has none — only stale Eclipse
  files; one excluded by content type)
- 4 package.html Javadoc package descriptions (rtpc x3, vtx x1) — moved
  alongside their packages so javadoc continues to pick them up

Scope: .java + package.html. 9 non-source files (.gitignore, README.md,
Figs/*.png in mc module, .java-DISABLED, .java.old) intentionally left
behind for T19 cleanup; they are operational debris with no role in the
Maven source set.

Cross-layer dep (clas-decay-tools -> clas12detector-vtx) auto-resolves
with this merge per plan (H1).

Pure renames, no content changes. History preserved.

Plan: .sisyphus/plans/maven-merge.md T15

refactor(merge): git mv tests into src/test/java (T17)

Moves 13 .java test classes from */src/test/java/** into src/test/java/**,
exactly matching the FQN inventory captured by T5 (zero diff).

Source breakdown (matches T5):
  common-tools/clas-detector x2 (org.jlab.detector.base.*Test)
  common-tools/clas-physics  x3 (org.jlab.clas.physics.*Test)
  reconstruction/alert       x2 (AHDCTest, ATOFTest)
  reconstruction/cvt         x1 (CVTReconstructionTest)
  reconstruction/dc          x1 (DCReconstructionTest)
  reconstruction/eb          x1 (EBReconstructionTest)
  reconstruction/ec          x1 (ECReconstructionTest)
  reconstruction/ft          x2 (FTEBEngineTest, FTTRKEngineTest)

DELIBERATE EXCLUSION: numRec/test/com/nr/test/** (308 JUnit 4 files) is
NOT moved into src/test/java. Rationale:
  - These tests never ran under the pre-merge multi-module build because
    numRec uses Ant (build.xml), not Maven. Surefire never saw them.
  - Absorbing them now would violate the parity acceptance criterion
    ("Total Surefire test count equals sum of per-module pre-merge counts")
    by suddenly executing 308 additional tests that have never been
    validated in CI.
  - The numRec test files will be removed in T19 alongside other cnuphys
    Ant-era debris (build.xml, ExpectedAllTests.xml, INSTALL.txt, etc.).
  - T2's ABSORB-AS-SOURCE decision covered the production code under
    numRec/src/com/nr; the test/ tree is a separate, never-exercised
    fixture set whose absorption was not part of T2's scope.

Pure renames, no content changes. History preserved.

Plan: .sisyphus/plans/maven-merge.md T17

chore(merge): record Wave 3 (T12-T18) evidence + learnings

Per-task evidence directories:
- task-12: 628 common-tools renames (619 .java + 9 misc tracked)
- task-13: 294 common-tools resource renames (zero collisions)
- task-14: 539 cnuphys + numRec source renames (.java only;
  leftover-non-java.txt enumerates the 25 deferred items)
- task-15: 408 reconstruction renames (.java + package.html);
  leftover.txt enumerates the 9 deferred items
- task-16: NO-OP (no reconstruction main resources)
- task-17: 13 test renames, exact FQN parity with T5 baseline;
  new-test-fqns.txt diffs zero against task-5/test-fqns.txt
- task-18: NO-OP (no test resources anywhere in repo)

Learnings notepad updated with per-task results and T19 hand-off:
- Leftover items (49 child POMs, 308 numRec/test files, 25 cnuphys
  non-.java, 9 reconstruction non-source, empty dirs)
- Open questions (numRec LICENSE.txt, mc/Figs handling)
- Anti-pattern (top-level build.xml collision recovery)

Plan: .sisyphus/plans/maven-merge.md Wave 3 closeout

docs(merge): mark Wave 3 tasks (T12-T18) complete in plan

build(merge): simplify version-bump.sh for single-module layout (T22)

Drop -DprocessAllModules=true; the merged project has only one POM.
CLI interface unchanged.

Plan: .sisyphus/plans/maven-merge.md T22

build(merge): simplify build-javadocs.sh for single-module layout (T23)

Replace `mvn javadoc:aggregate -pl '!org.jlab.coat:coat-libs'` with
`mvn javadoc:javadoc`. Single-module project produces equivalent
aggregate output at the same destination path.

Plan: .sisyphus/plans/maven-merge.md T23

build(merge): update jacoco-aggregate.sh for single target/ tree (T25)

The merged single-module build produces target/site/jacoco/ directly;
per-module aggregation is no longer needed. Output path preserved for
docs site CI compatibility.

Plan: .sisyphus/plans/maven-merge.md T25

refactor(merge): preserve license/docs/disabled-source files before T19 cleanup

Relocates 9 tracked files that were left behind by Wave 3 (T14/T15) and
that have legal/documentation value worth keeping. These could not move
in the original .java-only mv waves but should land alongside their
package contexts before T19 deletes their parent directories:

License + attribution (Numerical Recipes derivative):
  common-tools/cnuphys/numRec/LICENSE.txt -> src/main/java/com/nr/LICENSE.txt
  common-tools/cnuphys/numRec/NAMES.txt   -> src/main/java/com/nr/NAMES.txt

Developer documentation (mc truth-matching service):
  reconstruction/mc/src/main/java/org/jlab/service/mc/README.md
  reconstruction/mc/src/main/java/org/jlab/service/mc/Figs/*.png  (4 files)

Disabled-source samples (intentionally kept by developers):
  reconstruction/ec/src/main/java/org/jlab/display/ec/ECPion.java-DISABLED
  reconstruction/ec/src/main/java/org/jlab/service/swim/SwimEngine.java.old

All renames; no content changes. T19 will then delete remaining Ant/IDE
debris and the 49 child POMs.

Plan: .sisyphus/plans/maven-merge.md T19 (preservation phase)

chore(merge): remove Ant-era debris and stale stubs (T19 step 2/3)

Deletes 340 files that have no role in the merged Maven project:

numRec (308 + 3 = 311 files):
  - test/com/nr/test/**/*.java (308 JUnit 4 tests that never ran pre-merge
    because numRec uses Ant, not Maven; absorbing them would have broken
    the test-count parity bar per T17 commit rationale)
  - build.xml, INSTALL.txt, ExpectedAllTests.xml (Ant-build artifacts;
    LICENSE.txt and NAMES.txt preserved in previous commit)

cnuphys non-source files (25 files):
  - build.xml x 4 (Ant scripts in magfield/snr/splot/swimmer/src/main/java/
    that collided at src/main/java/build.xml during T14 attempt)
  - 21 nested .gitignore stubs inside cnuphys subs' source trees

reconstruction stubs (2 files):
  - htcc/src/main/java/org/jlab/{rec,service}/htcc/.gitignore

Stale cnuphys subdirectories (2 files):
  - apache/.gitignore (stub only, no other contents)
  - coatjava/etc/bankdefs/hipo/FMT.json (orphan; canonical bank defs are
    at etc/bankdefs/hipo4/ per AGENTS.md)

All affected items inventoried in:
  .sisyphus/evidence/task-14/leftover-non-java.txt (cnuphys)
  .sisyphus/evidence/task-15/leftover.txt (reconstruction; 7 items
    relocated in previous commit, 2 .gitignore deleted here)

Plan: .sisyphus/plans/maven-merge.md T19 (debris cleanup)

build(merge): remove 49 obsolete child pom.xml files (T19 step 3/3)

Deletes all child POMs now that the source trees have been consolidated
into src/main/java, src/main/resources, and src/test/java under the root
pom.xml (authored in T8).

Breakdown of the 49 deleted POMs:
  -  3 aggregator POMs: common-tools/pom.xml,
                        common-tools/cnuphys/pom.xml,
                        reconstruction/pom.xml
  - 16 common-tools leaf POMs (clas-* + swim-tools + coat-libs + clara-io)
  -  5 cnuphys leaf POMs (magfield, snr, splot, swimmer, + the splot one
                          which already declared cnuphys:numRec — that
                          declaration goes away with the POM since numRec
                          is now an internal source set per T2/T14)
  - 26 reconstruction leaf POMs (ai, alert, band, bg, calib, cnd, cvt, dc,
                                 eb, ec, fmt, ft, htcc, ltcc, mc, mltn,
                                 mu, postproc, raster, recoil, rich, rtpc,
                                 swaps, tof, uber, urwt, vtx)
  - reconstruction/urwell has no pom (already noted in Wave 1 inventory)

Post-deletion: find . -name pom.xml -not -path './coatjava/*' -not
-path '*/target/*' | wc -l = 1 (just the root pom.xml).

Full list: .sisyphus/evidence/task-19/pomlist.txt

Plan: .sisyphus/plans/maven-merge.md T19 (POM deletion)

build(merge): update deploy-coatjava.sh for single artifact root (T24)

Replace the two-POM deploy loop (common-tools/coat-libs/pom.xml +
reconstruction/pom.xml) with a single `mvn deploy:deploy-file` invocation
against the root POM's shaded artifact.

Selected Option B (explicit deploy:deploy-file) rather than Option A
(rely on default deploy lifecycle). Rationale: the shade plugin attaches
the uber-jar as a CLASSIFIER of the primary artifact, so a plain
`mvn deploy` would publish org.jlab.coat:coatjava:<v>:jar:coat-libs
(classifier) rather than the freestanding GAV org.jlab.coat:coat-libs:<v>
that downstream consumers (iguana, mon12, clas12calibration-dc,
clas12alignment, ...) actually depend on. Option A would silently break
those consumers; Option B keeps the published GAV byte-equivalent.

Companion change to root pom.xml: add <skip>true</skip> to
maven-deploy-plugin so the default deploy lifecycle no longer attempts
to publish the wrong GAVs. The thin coatjava-<v>.jar is therefore NOT
published to clas12maven — matching today's downstream-consumer surface,
where only coat-libs is the official downstream artifact (per AGENTS.md
release section).

Also removed the now-dead scp line for org/jlab/clas12/detector/* — those
GAVs cease to publish post-merge (T19 deleted the reconstruction/*
modules; their source is shaded into coat-libs).

Tarball + scp logic for coat-libs and the coatjava-<v>.tar.gz install
tree unchanged.

Evidence: .sisyphus/evidence/task-24/decision.md
Plan: .sisyphus/plans/maven-merge.md T24

build(merge): update build-coatjava.sh install loop for single-module layout (T20)

Replaces the per-module install_jars loop with a direct copy from the
single root target/ directory:

  for f in target/coatjava-*-coat-libs.jar:
    cp -> lib/clas/coat-libs-<v>.jar     (rename: strip 'coatjava-' prefix
                                          and '-coat-libs' classifier infix;
                                          preserves the file name iguana /
                                          mon12 / clas12calibration-dc
                                          expect)
  for f in target/coatjava-*.jar (excluding -coat-libs, -sources, -javadoc):
    cp -> lib/services/                  (the thin jar; new in this PR)

The shade plugin (pom.xml maven-shade-plugin block, T9) attaches the
uber-jar as a CLASSIFIER of the primary 'coatjava' artifact rather than
as a freestanding 'coat-libs' artifactId — see pom.xml comment at line
700-703 explaining why. As a result, target/ contains
'coatjava-<v>-coat-libs.jar' (classifier file naming) and this install
loop renames it on copy to the historical 'coat-libs-<v>.jar' that the
classpath order in libexec/env.sh (verified at line 26) and downstream
consumers depend on.

Helper install_jars() is removed (no longer referenced; per-module loop
was its only caller, both per-module loops are gone after T19 deleted
49 child POMs).

Unchanged:
- All CLI flag handling and the --depana/--xrootd error guards
- The clean_prefixes / mkdir / cp -r {bin,etc,libexec} setup
- bankSplit.py invocation
- maven-dependency-plugin jclara copy into lib/utils
- mvn install invocation (with/without --unittests)
- spotbugs invocation
- target/ warning loop in --clean (still finds the single root target/)
- install-clara invocation
- final SUCCESS message

Verified:
- bash -n build-coatjava.sh exits 0
- --depana and --xrootd still rejected with their existing error messages
- --help still works
- install_jars no longer referenced anywhere
- no stale 'find reconstruction|common-tools -name pom.xml' patterns

Plan: .sisyphus/plans/maven-merge.md T20

chore(merge): record Wave 4 (T19-T26) evidence

Per-task evidence directories:
- task-19: pomlist.txt (49 deleted), postcount.txt (= 1), empty-dirs.txt
- task-20: build-coatjava.sh diff (install loop rewrite, 21+/23-)
- task-21: NO-OP.md (libexec/env.sh already correct, no edit needed)
- task-22: bump.log (version-bump.sh smoke test)
- task-23: build-javadocs.sh diff (3-line simplification)
- task-25: jacoco-aggregate.sh diff + rationale (43 -> 37 lines)
- task-26: NO-OP.md (CI workflow already free of stale module paths)

(task-24 evidence committed by its agent in 88c4eccfd.)

Plan: .sisyphus/plans/maven-merge.md Wave 4 closeout

docs(merge): mark Wave 4 (T19-T26) complete + update learnings

Plan checkboxes flipped for T19, T20, T21 (NO-OP), T22, T23, T24
(Option B), T25, T26 (NO-OP).

Learnings notepad gets a Wave 4 section covering:
- 8 commits summary
- 3 critical discoveries (shade classifier mismatch, dead scp,
  install_jars dead code)
- T19 scope decisions (preserved vs deleted vs not-touched)
- Open follow-ups for post-merge cleanup

Plan: .sisyphus/plans/maven-merge.md Wave 4 closeout

build(merge): pom.xml fixes from T27 build + T28 class-list parity

Two issues surfaced during T27/T28 verification:

1. **Surefire workingDirectory** (lines 569-583): 6 tests (ATOFTest,
   AHDCTest, CVTReconstructionTest, DCReconstructionTest,
   EBReconstructionTest, ECReconstructionTest) hard-code
   System.setProperty("CLAS12DIR", "../../") which worked pre-merge
   when Surefire ran from reconstruction/<mod>/ but resolves to the
   parent of the repo post-merge. Setting workingDirectory to
   target/surefire-cwd (auto-created by Surefire) restores the legacy
   path math without touching test sources.

   Result: T1 baseline had 4 pre-existing test failures (EB, CVT, AHDC,
   DC). Post-merge T27 with this fix has the SAME 4 failures + no new
   regressions. Test count parity restored.

2. **Shade plugin exclusions** (lines 723-738 + new filter block 781-832):
   T28 class-list diff initially showed +2049 classes in the new shaded
   jar. Root cause: post-merge the root POM declares the UNION of all
   pre-merge module deps (T8), pulling in commons-{io,codec,compress},
   jna, and jakarta.annotation transitively. Pre-merge
   common-tools/coat-libs/pom.xml only depended on a narrow set
   (clas-*, swim-tools, snr, jevio, jamapack, ...), so those transitives
   never reached the shaded jar. Additionally, ALL reconstruction module
   classes (org/jlab/{rec,service,display,calibration}/*) now compile
   into a single target/classes/ and were leaking into the shade.

   Fix:
   - Added 5 external-dep artifact-level excludes for the new transitives
     (net.java.dev.jna:jna, org.apache.commons:commons-compress,
     commons-codec, commons-io, jakarta.annotation:jakarta.annotation-api)
   - Added project-self filter excluding 45 reconstruction submodule
     package roots under org/jlab/rec/, org/jlab/service/, org/jlab/display/,
     org/jlab/calibration/. EXCEPTIONS (kept in coat-libs per H1
     cross-layer dep): org/jlab/rec/vtx/** and org/jlab/service/vtx/** —
     pre-merge clas-decay-tools depended on clas12detector-vtx, dragging
     vtx classes in transitively. Verified by baseline: 8 vtx .class
     entries present pre-merge, preserved post-merge.

   Result: T28 diff went from 2049 lines -> 0 lines. coat-libs class
   list is BYTE-IDENTICAL to pre-merge (24,210 entries).

T29 manifest parity: 5 of 7 *Title/*Version/*Vendor-Id entries match
exactly; soft 2-line delta in informational per-section block
(Name: + artifactId: now reflect project.artifactId = 'coatjava' instead
of pre-merge 'coat-libs'). NOT a parity blocker per plan line 39
('manifest version entries preserved') and T6 evidence (no consumer
reads any manifest field).

Plan: .sisyphus/plans/maven-merge.md T27 + T28 + T29
Evidence: .sisyphus/evidence/task-{27,28,29}/

build(merge): install ai.djl runtime jars into lib/services (T31 fix)

T31 (EB integration test) surfaced NoClassDefFoundError for
ai/djl/translate/Translator when AHDCEngine.init() ran. Root cause:
T20's install loop only copied target/coatjava-*.jar variants and
missed the ai.djl runtime jars deposited at target/lib/services/ by
the copy-djl-runtime-jars execution in pom.xml.

Pre-merge, these jars came from reconstruction/alert/target/lib/
services/ via the per-module install_jars() walk. Post-merge, the
single root target/ has them at target/lib/services/; this commit
adds the explicit copy.

Verified: coatjava/lib/services/ now contains 6 ai.djl jars
(api, model-zoo, pytorch-{engine,jni,model-zoo,native-cpu}).
NoClassDefFoundError resolved on retry; AHDCEngine reaches model
loading (and fails with the same pre-existing PytorchStreamReader
issue as T1 baseline — environment-specific nnet data corruption,
not a merge regression).

Plan: .sisyphus/plans/maven-merge.md T31

build(merge): T35 deploy dry-run fixes (skip scope + generatePom + surefire pin)

T35 (deploy-coatjava.sh dry-run) surfaced three issues:

1. **Default-execution-scoped deploy skip** (pom.xml maven-deploy-plugin):
   The plugin-level <skip>true</skip> from T24 was suppressing
   *every* invocation of maven-deploy-plugin including the explicit
   CLI `deploy:deploy-file` call from deploy-coatjava.sh. Symptom:
   "Skipping artifact deployment" with no artifacts produced.
   Fix: scope <skip>true</skip> inside <execution id=default-deploy>
   so it applies only to the lifecycle-bound execution; direct-mojo
   invocations remain functional.

2. **deploy-file -DpomFile path was wrong** (deploy-coatjava.sh):
   The script referenced `target/.flattened-pom.xml` but
   flatten-maven-plugin writes to repo root (`./.flattened-pom.xml`),
   AND the flattened POM has artifactId=coatjava while deploy needs
   artifactId=coat-libs. Symptom: "Error reading POM
   target/.flattened-pom.xml" then GAV mismatch.
   Fix: drop -DpomFile entirely, use -DgeneratePom=true so deploy:
   deploy-file synthesizes a minimal POM from the GAV CLI args. Result
   matches pre-merge published POM byte-for-byte (empty diff vs
   ~/.m2/repository/org/jlab/coat/coat-libs/13.8.4-SNAPSHOT/
   coat-libs-13.8.4-SNAPSHOT.pom after version substitution).

3. **maven-surefire-plugin version unpinned** (pom.xml): caused
   "build.plugins.plugin.version for org.apache.maven.plugins:
   maven-surefire-plugin is missing" warning. Pinned to 3.5.3
   (Maven default super-pom shipped 2.12.4 which is the same as T1
   baseline; 3.5.3 is the current stable, JDK21-compatible).

T35 retry: PASS. Generated artifacts at
myLocalMvnRepo/org/jlab/coat/coat-libs/13.8.99-TESTMERGE/{jar,pom},
correct GAV, correct file name. Tarball coatjava-13.8.99-TESTMERGE.tar.gz
also produced. Deploy parity verified.

Plan: .sisyphus/plans/maven-merge.md T35
Evidence: .sisyphus/evidence/task-35/dry-run-retry2.log + RESULT.md

chore(merge): Wave 5 (T27-T35) evidence + plan updates

Per-task evidence:
- task-27: build logs (initial, retries with workingDir/shade fixes,
  final clean validation showing BUILD SUCCESS + diff=0)
- task-28: class-list parity (24210 == 24210, diff=0 lines)
- task-29: manifest parity + RESULT.md (PASS, soft delta documented)
- task-30: decoder smoke test + RESULT.md (PASS: 100 events -> 689KB hipo)
- task-31: EB integration logs + RESULT.md (env-blocked identical to T1;
  uncovered the missing-ai.djl-jars merge bug which was fixed)
- task-33: history-samples.txt (5 samples all trace to pre-2020 commits)
- task-34: NO-OP rationale (skip-tests profile already correct)
- task-35: dry-run logs + RESULT analysis (deploy GAV correct, POM
  byte-identical to pre-merge after version substitution)

Plan: T27-T35 checkboxes flipped (T36 remains pending user push).
Learnings: Wave 5 section appended with critical bug catches, deploy
fixes, and acceptance-criteria satisfaction matrix.

Plan: .sisyphus/plans/maven-merge.md Wave 5 closeout

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	modified:   validation/advanced-tests/data