feat(analysis): add question-shaped run queries

[andreasronge]

Closes #1337

Summary

• replace the split log/inspection vocabularies with six question-shaped analysis/* operations
• share one bounded semantic read model across PTC-Lisp, the Viewer, Elixir embedders, and ptc transcript
• preserve separate public/private authority while adding snapshot correlation, complete internal pagination, aggregate result bounds, and typed transcript diagnostics
• remove raw Viewer inspection rendering and duplicate repo-analyst history aliases

Simplification and ease of use

• four prompt namespaces and 23 exports become one namespace with six operations
• repo-analyst run facade drops from 346 lines/13 join helpers to 52 lines/six question wrappers
• production read/command surface is 619 lines smaller against current origin/main (2,364 deleted; 1,745 added)
• conversation reconstruction is one semantic call; the flagship human path is one ptc transcript RUN_ID ... command with no record-shape knowledge
• the same immutable evidence semantics now drive PTC-Lisp, Viewer rendering, embedding callbacks, CLI transcripts, public-only runs, private post-mortems, incomplete captures, and trace-only runs

Rebase and CI fixes

• rebased onto current origin/main at be16ef00 (perf(cli): accelerate mix ptc startup (#1338))
• updated repo-analyst live coverage to use the named mission contract
• refreshed the replay prompt hash and supplied the required component-override environment
• declared the named default mission in the GitHub MCP integration fixture
• aligned Elixir-backed stdio fixture mission limits with installed discovery ceilings and constrained helper VMs to one scheduler under suite load
• accepted both truthful bounded launcher finish reasons when a clean exit races the termination boundary after final stdout
• aligned live E2E assertions with configured turn budgets, normalized provider narration, valid retry counts, and semantically equivalent extracted project names
• lengthened an unrelated caller-cancellation test deadline so full-suite scheduler pressure cannot let its worker time out before the cancellation assertion
• removed the completed disposable implementation plan while retaining durable contracts in docs/trace-log-contract.md

Review record

• audited requirements from Complete Slice E1 private inspection snapshots and correlated queries (local macOS) #1127, Add Slice E2 inspection-analysis-v1 private REPL profile (local macOS) #1129, feat(repl): add --private-unattended, a second authorized private destination #1218, --private-unattended --format jsonl with no input opens an interactive REPL, corrupting the JSONL stream #1220, A run can inspect its own process but not its own answer, blocking outcome-based self-critique #1223, fix(inspection): expose terminal run results #1323, Private inspection analysis is not closed under recursion #1324, Unsupported inspection schema version reports as invalid_snapshot #1330, CLI: every mix ptc invocation pays ~3.8 s of startup — three-project load, no-op compile check, and full CLI bootstrap even for --version #1336, and Refactor the trace/inspection read side: one query surface, question-shaped vocabulary, restore conversation retrieval (breaking changes welcome) #1337
• completed three plan reviews and four implementation-review passes, honoring the requested caps
• the implementation reviews identified 11 evidence-integrity, source-authority, Viewer-state, bounding, and error-classification gaps; all were addressed
• final independent review: approved with no remaining actionable findings

Verification

• mix precommit: 6,212 root checks/tests plus Viewer, package, launcher, release, specs, conformance, duplication, and generated-artifact gates
• MIX_ENV=dev mix docs --warnings-as-errors
• pre-push hook: 6,212 root tests, Viewer 44 tests, Credo, generated artifacts, upstream audit, and Dialyzer (0 errors)
• affected live Integration tests reproduced locally and passed after the fixes
• caller-cancellation regression repeated 20 times at the failing seed
• focused source-policy and immutable-capture regression suite: 85 tests