feat: harden autonomy lifecycle, OOM bounds, and provider-boundary finalization

This PR consolidates a coordinated batch of fixes around autonomy run/flow lifecycle, scheduled task deduplication, provider-boundary state finalization, and matching memory-bound treatments for adjacent long-running subsystems (REPL fullscreen scrollback, skill-search/skill-learning runtime activation). All changes were developed and reviewed together because they touched the same lifecycle invariants and were uncovered by the same long-running session reproductions.

## Lifecycle correctness

- Queued autonomy prompts are not injected unless the persisted run was successfully claimed; queued run claiming is now terminal-safe so a once-consumed/cancelled/failed run can not slip back into `queued`.
- Autonomy run/flow finalization happens on completion, provider error, generator close, and cancellation — not just the happy path. New `src/__tests__/queryAutonomyProviderBoundary.test.ts` covers these provider-boundary transitions.
- `requestManagedAutonomyFlowCancel` and `resumeManagedAutonomyFlowPrompt` carry `rootDir` and `currentDir` explicitly across detached async boundaries (proactive-tick, cron, daemon restart) instead of inferring from process state.
- Active runs/flows are protected from janitor pruning so a running step can not be garbage-collected mid-flight (`src/utils/autonomyAuthority.ts`).
- Heartbeat parser now ignores fenced code blocks; the two-phase commit window for autonomy state transitions is documented in `docs/internals/autonomy-jira.md`.

## Ownership and dedup

- `src/utils/autonomyRuns.ts`: ownership stamping (run id + rootDir carried end-to-end), source-based dedup against active runs.
- `src/hooks/useScheduledTasks.ts`: scheduled ticks deduplicate against runs already active on the same source label.
- `src/utils/processUserInput/processSlashCommand.tsx`: forked slash commands now thread the autonomy `runId` so completion finalizers can find the originating run for deferred completion.
- New `src/utils/autonomyQueueLifecycle.ts` and tests collect the queue-side lifecycle invariants in one place.

## Memory bounds (related, same review pass)

- `src/screens/REPL.tsx`: caps fullscreen scrollback after the compact boundary and updates trailing progress rows in place. Long-running fullscreen sessions could otherwise retain thousands of post-compaction messages and duplicate progress rows, keeping Ink trees alive long after their useful context had moved on.
- `src/services/skillSearch/*` and `src/services/skillLearning/*`: runtime activation is strictly opt-in via existing env toggles; session caches are capped so long-running processes can not grow them forever. Build presence is preserved so operators can still discover and opt into the slash commands.

## CI / test contract

- `tests/integration/dependency-overrides.test.ts`: smoke test no longer drives Mermaid's browser renderer; it validates the package-resolution contract directly so CI does not regress on unrelated browser timing.
- New `tests/integration/autonomy-lifecycle-user-flow.test.ts`: end-to-end CLI subprocess flow exercising `status --deep`, `flows`, `flow <id>`, `flow resume`, `flow cancel` against persisted state.
- `src/entrypoints/cli.tsx`: `claude autonomy …` routes through an entrypoint fast path that reuses the slash-command formatter without booting the full interactive CLI. Stdout is flushed before forced exit so coverage subprocesses do not terminate with empty stdout.
- `packages/builtin-tools/src/tools/RemoteTriggerTool/__tests__/RemoteTriggerTool.test.ts`: stabilized to prevent audit flake under coverage.

## Tests added

- `src/__tests__/queryAutonomyProviderBoundary.test.ts`
- `src/hooks/__tests__/useScheduledTasks.test.ts`
- `src/utils/__tests__/autonomyAuthority.test.ts`
- `src/utils/__tests__/autonomyFlows.test.ts` (extended)
- `src/utils/__tests__/autonomyPersistence.test.ts` (extended)
- `src/utils/__tests__/autonomyQueueLifecycle.test.ts`
- `src/utils/__tests__/autonomyRuns.test.ts` (extended)
- `src/utils/processUserInput/__tests__/processSlashCommand.test.ts`
- `tests/integration/autonomy-lifecycle-user-flow.test.ts`

## Docs

- `docs/agent/sur-loop-scheduled-oom.md`: System Understanding Report covering the scheduled/loop OOM problem, the call graphs investigated, and the lifecycle invariants this PR establishes.
- `docs/agent/sur-skill-overflow-bugs.md`: SUR for the related skill-overflow context.
- `docs/internals/autonomy-jira.md`: documents the two-phase commit window and ownership stamping invariants.
- `docs/memory-leak-audit.md`: audit notes covering the REPL/scrollback and skill-search bounds.

## Invariants this PR establishes

1. Queued autonomy prompts are not injected unless the persisted run was successfully claimed.
2. Terminal run/flow states are terminal — completion, failure, and cancellation all finalize state regardless of which provider/error path triggered them.
3. Autonomy run/flow `rootDir` is carried explicitly across detached async boundaries instead of inferred from a shared singleton.
4. State-only CLI subcommands (`autonomy status|runs|flows|flow …`) bypass full interactive bootstrap so they do not hold unrelated handles open.
5. REPL fullscreen scrollback and skill-search/skill-learning session caches are explicitly bounded.

## Validation

```bash
bun run typecheck
CI=true GITHUB_ACTIONS=true bun test            # 3996 pass / 0 fail across 305 files
bun test src/__tests__/queryAutonomyProviderBoundary.test.ts \
         src/hooks/__tests__/useScheduledTasks.test.ts \
         src/utils/__tests__/autonomy{Runs,Flows,Authority,QueueLifecycle,Persistence}.test.ts \
         src/utils/processUserInput/__tests__/processSlashCommand.test.ts \
         tests/integration/autonomy-lifecycle-user-flow.test.ts
```

## Origin

This PR is the consolidated, upstream-targeted version of two fork-side review PRs (fix/loop-scheduled-autonomy-oom and fix/autonomy-lifecycle). The fork-side review history is preserved at https://github.com/amDosion/claude-code-bast/pull/7 . The fork's own internal `chore: keep fork current with upstream` sync commits and the `docs: update contributors` automation are intentionally not included in this PR.

The autonomy CLI handler `rootDir` threading that the fork added (78f64d8a, 98d04ddb) is intentionally omitted here because upstream `a2cfaf91` (fix: 修复 RemoteTriggerTool 和 autonomy 测试的全量运行失败) already performed the equivalent change with an additional `currentDir` option. Keeping the upstream version avoids regressing that improvement.

src/services/skillSearch/prefetch.ts

@@ -14,9 +14,35 @@ import { readFile } from 'node:fs/promises'
 import { join } from 'node:path'
 import { parseFrontmatter } from '../../utils/frontmatterParser.js'
 
+/**
+ * Per-session memoization to avoid re-emitting the same skill discovery /
+ * gap signal twice. Each Set is bounded to keep long-running sessions from
+ * monotonically accumulating skill names and signal keys forever (which
+ * was the original session-scoped-but-unbounded design).
+ *
+ * FIFO eviction by insertion order — once the cap is hit, the oldest
+ * entries roll off and may be re-recorded if rediscovered, which is the
+ * correct degraded behaviour: at worst we re-emit a duplicate signal,
+ * never silently drop a real one.
+ */
+const SESSION_TRACKING_MAX = 1000
+const SESSION_TRACKING_TRIM_TO = 750
 const discoveredThisSession = new Set<string>()
 const recordedGapSignals = new Set<string>()
 
+function addBoundedSessionEntry(set: Set<string>, value: string): void {
+  set.add(value)
+  if (set.size > SESSION_TRACKING_MAX) {
+    const toDrop = set.size - SESSION_TRACKING_TRIM_TO
+    const iter = set.values()
+    for (let i = 0; i < toDrop; i++) {
+      const next = iter.next()
+      if (next.done) break
+      set.delete(next.value)
+    }
+  }
+}
+
 const AUTO_LOAD_MIN_SCORE = Number(
   process.env.SKILL_SEARCH_AUTOLOAD_MIN_SCORE ?? '0.30',
 )
@@ -185,7 +211,7 @@ async function maybeRecordSkillGap(
 
   const gapSignalKey = `${trigger}:${queryText.trim().toLowerCase()}`
   if (recordedGapSignals.has(gapSignalKey)) return undefined
-  recordedGapSignals.add(gapSignalKey)
+  addBoundedSessionEntry(recordedGapSignals, gapSignalKey)
 
   try {
     const [{ isSkillLearningEnabled }, { recordSkillGap }] = await Promise.all([
@@ -241,7 +267,7 @@ export async function startSkillDiscoveryPrefetch(
     const newResults = results.filter(r => !discoveredThisSession.has(r.name))
     if (newResults.length === 0) return []
 
-    for (const r of newResults) discoveredThisSession.add(r.name)
+    for (const r of newResults) addBoundedSessionEntry(discoveredThisSession, r.name)
 
     const signal: DiscoverySignal = {
       trigger: 'assistant_turn',
@@ -305,7 +331,7 @@ export async function getTurnZeroSkillDiscovery(
 
     if (results.length === 0 && !gap) return null
 
-    for (const r of results) discoveredThisSession.add(r.name)
+    for (const r of results) addBoundedSessionEntry(discoveredThisSession, r.name)
 
     const signal: DiscoverySignal = {
       trigger: 'user_input',