Fix Shepherd/JDO connection leaks causing stuck dbconnections entries

[JasonWildMe]

Summary

Fixes a set of PersistenceManager / connection leaks observed on production Sharkbook and Flukebook via dbconnections.jsp (stuck entries at IBEISIA.processCallback:rollback, RestServlet:new, plus in-flight Encounter.opensearchDocumentSerializer:begin and api.Bulk.doGet:begin).

The single commit (993a81e) touches five files with +184 / -150 lines (functional changes only — ignoring CRLF→LF noise in the rest of the tree):

• Shepherd.closeDBTransaction / rollbackDBTransaction — move the ShepherdState writes into finally blocks so state always advances past "begin". When pm.close() or rollback() throws, the entry now stays as "close-failed" / "rollback-failed" so the dashboard preserves diagnostic evidence instead of either silently losing it or getting stuck at "begin".
• IBEISIA.processCallback — wrap both Shepherds in try { ... } finally { rollbackAndClose(); }. The bare return rtn; on the no-log path (the source of the IBEISIA.processCallback:rollback stuck entries) now runs the finally. Setup moved inside the try for consistency.
• RestServlet.doPost / doDelete / doHead — outer try/finally around each method body removes the RestServlet.class_<id> state entry on every return path, including doPost's empty-body 400 early return. Fixes the accumulating RestServlet:new entries.
• BulkImport.doGet / doPost — Shepherd construction / setAction / beginDBTransaction moved inside the try with a null-safe finally. Background-thread inner class captures bgContext as final.
• OpenSearch.setPermissionsNeeded / setActive / unsetActive / updatePermissionsIndex / updateEncounterIndexes — same try-with-null-safe-finally hardening.

Flagged as follow-up (not in this PR)

• OpenSearch indexing fan-out — per-object Executors.newFixedThreadPool(4) in Encounter/MarkedIndividual/Occurrence opensearchIndexDeep, plus a nested Shepherd created per Jackson serialization in Base.opensearchDocumentSerializer(jgen) — this multiplies concurrent DB transactions during indexing storms. It is what drives the 70+ in-flight Encounter.opensearchDocumentSerializer:begin entries. Needs a design pass (shared bounded executor + pass the outer Shepherd through serialization).
• commitDBTransaction swallows exceptions — separate correctness bug: IBEISIA.processCallback can still claim success=true after a silently-failed commit. Not a leak, so out of scope here.

Test plan

• mvn compile clean (verified locally)
• IBEISIA.processCallback: exercise the no-log early-return path, the successful detect path, and the "no annotations suitable for identification" path; confirm no stuck IBEISIA.processCallback:* entries accumulate on dbconnections.jsp
• RestServlet: POST (empty body + normal), DELETE, HEAD requests while watching dbconnections.jsp — confirm RestServlet:new no longer accumulates
• BulkImport list + detail doGet and doPost/doDelete flows
• Any reproducible pm.close() failure — confirm the dashboard shows close-failed rather than vanishing
• Monitor dbconnections.jsp on staging for 24h post-deploy; confirm entry count stabilizes

Credits

• Root cause investigation and implementation: Claude Opus 4.7 (Claude Code, 1M context)
• Independent plan review and code review: Codex CLI (OpenAI)
• Human: JasonWildMe

🤖 Generated with Claude Code and reviewed with Codex CLI

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 51.54%. Comparing base (606982f) to head (3070e41).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1553   +/-   ##
=======================================
  Coverage   51.54%   51.54%           
=======================================
  Files         308      308           
  Lines       11952    11952           
  Branches     3842     3833    -9     
=======================================
  Hits         6161     6161           
- Misses       5503     5510    +7     
+ Partials      288      281    -7     

Flag	Coverage Δ
backend	51.54% <ø> (ø)
frontend	51.54% <ø> (ø)

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