DeepSeek v4 in thinking mode sometimes returns reasoning_content: ""
when the model answers directly without internal reasoning. Two places
were filtering the empty string out, which dropped the thinking block
from the assistant turn entirely. The next request then omitted
reasoning_content for that prior turn, and DeepSeek rejected with
400 "reasoning_content ... must be passed back to the API".
Fix:
- openaiStreamAdapter: open a thinking block whenever reasoning_content
is present (including ""); skip the empty thinking_delta event since
the empty value is already conveyed by the block's initial state.
- openaiConvertMessages: preserve empty thinking blocks as
reasoning_content: "" when serializing assistant messages back to
the OpenAI/DeepSeek format.
Tests:
- New: empty reasoning_content opens a thinking block (adapter).
- Updated: empty thinking blocks now round-trip as reasoning_content: ""
instead of being dropped.
- New: assistant messages with no thinking block still omit
reasoning_content (regression guard for non-thinking models).
Root causes:
1. ThemeProvider was imported but never used in App.tsx and showSetupDialog
2. setThemeConfigCallbacks was never called to inject persistence callbacks
3. Preview/save/cancel theme lifecycle had no provider to coordinate
Changes:
- Export setThemeConfigCallbacks from @anthropic/ink
- Wrap App.tsx children with ThemeProvider (initialState from config, onThemeSave persists)
- Wrap showSetupDialog with ThemeProvider for onboarding/trust dialogs
- Call setThemeConfigCallbacks in init.ts to register load/save callbacks
- Update SnapshotUpdateDialog test to account for new ThemeProvider wrapper
Fixes #theme-switching
* 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.
* fixup: address CodeRabbit review on PR #386
Twelve actionable items (7 Major + 5 Minor) from the CodeRabbit review on
claude-code-best/claude-code#386:
- docs/internals/autonomy-jira.md: typo "due input close" → "due to input close".
- src/utils/autonomyRuns.ts:
- selectPersistedAutonomyRuns no longer evicts active (queued/running) runs
when the combined list exceeds AUTONOMY_RUNS_MAX. Active runs are kept in
full and the inactive history is capped to the remaining budget so
persisted ownership for live work survives.
- isValidOwnerProcessId now allows pid <= 4_194_304 so a live run owned by
the maximum Linux PID is not treated as stale.
- src/utils/autonomyAuthority.ts: maskCodeFencedLines tracks the active fence
length and only closes the fence when a same-character run of equal-or-
greater length appears with no trailing content, so a nested ```yaml inside
an outer ```` block no longer leaks fake `tasks:` entries into the parser.
- src/cli/print.ts: late-shutdown branches in the cron and scheduled-task
paths now call cancelQueuedAutonomyCommands({ commands: [command] }) instead
of markAutonomyRunCancelled(...). Updating run state alone left the
queue-side record orphaned for resume/recovery.
- src/utils/processUserInput/processSlashCommand.tsx: scheduled-task-result
notification is enqueued before finalizeAutonomyRunCompleted (which queues
follow-up autonomy commands) so both at priority: 'later' land in order and
the next autonomy step can not run before the worker's output is observed.
- src/screens/REPL.tsx + src/utils/handlePromptSubmit.ts:
- onQuery now returns Promise<boolean>: false from the concurrent-guard
skip path, true otherwise. Other call sites use `void onQuery(...)` and
are unaffected. handlePromptSubmit's onQuery prop type matches.
- The autonomy-prompt callsite captures the executed flag, finalizes
claim.claimedCommands as { type: 'completed' } only when onQuery actually
ran, and runs the completed-finalize in its own try/catch so a failure
there does not propagate into the outer catch and trigger a second
finalize as { type: 'failed' } for the same commands.
- Removed the unsafe `command.value as string` cast; createUserMessage
already accepts `string | ContentBlockParam[]`.
- createUserMessage mock in src/__tests__/handlePromptSubmit.test.ts now
matches the new Promise<boolean> shape.
- packages/builtin-tools/src/tools/RemoteTriggerTool/__tests__/
RemoteTriggerTool.test.ts:
- Inline auth mock replaced with the shared tests/mocks/auth (added).
- The full mock of src/constants/oauth.js is replaced by a narrow
side-effect-only mock that overrides the env-reading helpers
(getOauthConfig, fileSuffixForOauthConfig, MCP_CLIENT_METADATA_URL) and
delegates pure data exports to the real module.
- tests/integration/dependency-overrides.test.ts:
- mermaid does not export `./package.json` in its exports map, so
require.resolve('mermaid/package.json') throws
ERR_PACKAGE_PATH_NOT_EXPORTED in runtimes that honor exports semantics.
The test now resolves the package entry and walks up to the package
root via a small findPackageJson helper.
- readFileSync from node:fs is replaced with `await Bun.file(...).text()`
to match the project's Bun-API requirement.
Validation:
- bun run typecheck (clean).
- bun test → 3996 pass / 0 fail across 305 test files.
Targets PRs:
- amDosion/claude-code-bast#8 (fork-internal review)
- claude-code-best/claude-code#386 (upstream review, same head branch)
* fixup: address CodeRabbit second-round review on PR #386
Four inline + one outside-diff actionable comment from the second CodeRabbit
review on claude-code-best/claude-code#386:
- tests/mocks/auth.ts: align mock return contracts with src/utils/auth.ts.
checkAndRefreshOAuthTokenIfNeeded resolves to a Promise<boolean> and
getClaudeAIOAuthTokens returns the full token shape (refreshToken, expiresAt,
scopes, subscriptionType, rateLimitTier) so tests that branch on these
values can not silently drift away from production.
- src/utils/handlePromptSubmit.ts (461-468): clear the freshly-published
abortController before the early return when every claimed autonomy command
was skipped as non-consumable, so this turn's stale controller does not leak
into the next turn.
- src/utils/handlePromptSubmit.ts (621-649): separate execution failure from
finalizer failure. The turn body now writes to a `turnError` slot; a single
pass after the inner try decides whether to finalize claimed commands as
`completed` or `failed`, with each finalize call wrapped in its own
try/catch so a failure inside finalize does not flip a successful turn into
`failed` and double-finalize the same commands. The outer catch only
rethrows the original turn error.
- src/utils/processUserInput/processSlashCommand.tsx (228-276): wrap the
post-success `finalizeDeferredAutonomyRunCompleted()` call in its own
try/catch so a finalize failure no longer falls into the worker-failure
catch path and emits a contradictory `<scheduled-task-result status="failed">`
for a slash command that actually succeeded.
Outside scope (not changed) — the CodeRabbit suggestion to add a `.ts`
extension to the shared `tests/mocks/auth` import contradicts the project's
existing convention: every other test imports the shared mocks without the
extension (e.g. `tests/mocks/log`, `tests/mocks/debug`,
`tests/mocks/file-system`), and the project's tsconfig does not enable
`allowImportingTsExtensions`, so adding the extension fails typecheck. The
import is kept extension-less to match the rest of the suite.
Validation:
- bun run typecheck (clean).
- bun test → 3996 pass / 0 fail across 305 test files.
* docs: 给 sur-skill-overflow-bugs 的代码块加 bash 标签
应用 PR #386 review 的剩余 nit。pid_max 边界、REPL cast、autonomy-jira typo
三处与远端 fixup (452a7e6) 内容相同，rebase 时已去重，本次提交仅包含 code
fence 语言标签这一项。
* fixup: 处理 PR #386 review 中尚未覆盖的 4 项
- src/cli/print.ts: cron onFire 改用 createAutonomyQueuedPromptIfNoActiveSource
并以 prompt 文本作为 sourceId，避免同一定时提示在前一次 run 仍活跃时被重复
入队叠加；顺手移除 4 个已没人引用的 dead import
(commitAutonomyQueuedPrompt / prepareAutonomyTurnPrompt /
markAutonomyRunCancelled / createAutonomyQueuedPrompt)
- src/services/compact/postCompactCleanup.ts: 在 void import().then() 处加
注释，明确 sweepFileContentCache 是有意的 fire-and-forget，函数对外保持
同步签名是设计而非疏忽
- src/utils/autonomyFlows.ts: 给 selectPersistedAutonomyFlows 的两阶段排序
加文档注释（先按 active+updatedAt 选 top-N，再统一按 updatedAt 重排）
- tests/integration/autonomy-lifecycle-user-flow.test.ts: stderr 断言失败时
把实际 stderr 内容写进 message，方便 CI 失败时定位
* refactor: 简化/复用/防御 — 清理 PR #386 审计发现
简化 (S1, S2):
- src/cli/print.ts: 抽出 dispatchHeadlessCronCommand 本地 helper，把
cron 三个入口（onFire / onFireTask agent / onFireTask 非-agent）共享的
「dedup-claim → input-close-recheck → onSuccess」管线集中到一处，
避免三个分支在「claim 与 dispatch 之间发生 inputClosed」的处理上漂移。
enqueueAndRun 再抽出来，使两个非-agent 分支共用一个 onSuccess 回调。
约 -55 行重复模板。
- src/utils/autonomyPersistence.ts: 新增 retainActiveFirst<T> 泛型
helper —— active 记录无条件保留（不参与 cap），inactive 按 timestamp
desc 填满剩余预算；统一 selectPersistedAutonomyRuns / Flows 的两阶段
排序语义。
- src/utils/autonomyRuns.ts、autonomyFlows.ts: 改用 retainActiveFirst，
删掉重复的内联两阶段排序逻辑。
复用 (R1, review #8):
- tests/mocks/file-system.ts: 新增 readTempFile / tempPathExists 两个
Bun.file 包装，补齐 Node fs.readFileSync / existsSync 在测试里的
Bun-only 等价物。
- src/utils/__tests__/autonomyRuns.test.ts: 把全部 Node fs/path 导入
（existsSync, readFileSync, mkdir, writeFile, path.join/resolve）替换为
tests/mocks/file-system 的共享 helper + node:path（带 node: 前缀）。
不再有 6 处 mkdir + writeFile 模板，统一用 writeTempFile（自带 mkdir-p）。
解决 review #8 (Major) 的 Bun-only 运行时契约违反。
防御 (D1, OOM 早期信号):
- src/services/compact/postCompactCleanup.ts: 在 void import().then() 末尾
补 .catch(logError)。当前 attributionHooks 是 stub，但当真实现被恢复
且 sweepFileContentCache 抛错时，这个 .catch 阻止它变成 unhandled
rejection（函数返回值是 void，调用者无从观察异步失败）。
- src/utils/autonomyRuns.ts: 给 active runs 加 100 条软上限 + 一次性
warn。selectPersistedAutonomyRuns 仍然永不淘汰 active 记录，但跨过
阈值时 logError 一次，作为 finalize-leak 早期信号——避免 active 无限
增长悄悄使 AUTONOMY_RUNS_MAX 失效。
---------
Co-authored-by: unraid <local@unraid.local>
Co-authored-by: Claude <noreply@anthropic.com>
Four inline + one outside-diff actionable comment from the second CodeRabbit
review on claude-code-best/claude-code#386:
- tests/mocks/auth.ts: align mock return contracts with src/utils/auth.ts.
checkAndRefreshOAuthTokenIfNeeded resolves to a Promise<boolean> and
getClaudeAIOAuthTokens returns the full token shape (refreshToken, expiresAt,
scopes, subscriptionType, rateLimitTier) so tests that branch on these
values can not silently drift away from production.
- src/utils/handlePromptSubmit.ts (461-468): clear the freshly-published
abortController before the early return when every claimed autonomy command
was skipped as non-consumable, so this turn's stale controller does not leak
into the next turn.
- src/utils/handlePromptSubmit.ts (621-649): separate execution failure from
finalizer failure. The turn body now writes to a `turnError` slot; a single
pass after the inner try decides whether to finalize claimed commands as
`completed` or `failed`, with each finalize call wrapped in its own
try/catch so a failure inside finalize does not flip a successful turn into
`failed` and double-finalize the same commands. The outer catch only
rethrows the original turn error.
- src/utils/processUserInput/processSlashCommand.tsx (228-276): wrap the
post-success `finalizeDeferredAutonomyRunCompleted()` call in its own
try/catch so a finalize failure no longer falls into the worker-failure
catch path and emits a contradictory `<scheduled-task-result status="failed">`
for a slash command that actually succeeded.
Outside scope (not changed) — the CodeRabbit suggestion to add a `.ts`
extension to the shared `tests/mocks/auth` import contradicts the project's
existing convention: every other test imports the shared mocks without the
extension (e.g. `tests/mocks/log`, `tests/mocks/debug`,
`tests/mocks/file-system`), and the project's tsconfig does not enable
`allowImportingTsExtensions`, so adding the extension fails typecheck. The
import is kept extension-less to match the rest of the suite.
Validation:
- bun run typecheck (clean).
- bun test → 3996 pass / 0 fail across 305 test files.
Twelve actionable items (7 Major + 5 Minor) from the CodeRabbit review on
claude-code-best/claude-code#386:
- docs/internals/autonomy-jira.md: typo "due input close" → "due to input close".
- src/utils/autonomyRuns.ts:
- selectPersistedAutonomyRuns no longer evicts active (queued/running) runs
when the combined list exceeds AUTONOMY_RUNS_MAX. Active runs are kept in
full and the inactive history is capped to the remaining budget so
persisted ownership for live work survives.
- isValidOwnerProcessId now allows pid <= 4_194_304 so a live run owned by
the maximum Linux PID is not treated as stale.
- src/utils/autonomyAuthority.ts: maskCodeFencedLines tracks the active fence
length and only closes the fence when a same-character run of equal-or-
greater length appears with no trailing content, so a nested ```yaml inside
an outer ```` block no longer leaks fake `tasks:` entries into the parser.
- src/cli/print.ts: late-shutdown branches in the cron and scheduled-task
paths now call cancelQueuedAutonomyCommands({ commands: [command] }) instead
of markAutonomyRunCancelled(...). Updating run state alone left the
queue-side record orphaned for resume/recovery.
- src/utils/processUserInput/processSlashCommand.tsx: scheduled-task-result
notification is enqueued before finalizeAutonomyRunCompleted (which queues
follow-up autonomy commands) so both at priority: 'later' land in order and
the next autonomy step can not run before the worker's output is observed.
- src/screens/REPL.tsx + src/utils/handlePromptSubmit.ts:
- onQuery now returns Promise<boolean>: false from the concurrent-guard
skip path, true otherwise. Other call sites use `void onQuery(...)` and
are unaffected. handlePromptSubmit's onQuery prop type matches.
- The autonomy-prompt callsite captures the executed flag, finalizes
claim.claimedCommands as { type: 'completed' } only when onQuery actually
ran, and runs the completed-finalize in its own try/catch so a failure
there does not propagate into the outer catch and trigger a second
finalize as { type: 'failed' } for the same commands.
- Removed the unsafe `command.value as string` cast; createUserMessage
already accepts `string | ContentBlockParam[]`.
- createUserMessage mock in src/__tests__/handlePromptSubmit.test.ts now
matches the new Promise<boolean> shape.
- packages/builtin-tools/src/tools/RemoteTriggerTool/__tests__/
RemoteTriggerTool.test.ts:
- Inline auth mock replaced with the shared tests/mocks/auth (added).
- The full mock of src/constants/oauth.js is replaced by a narrow
side-effect-only mock that overrides the env-reading helpers
(getOauthConfig, fileSuffixForOauthConfig, MCP_CLIENT_METADATA_URL) and
delegates pure data exports to the real module.
- tests/integration/dependency-overrides.test.ts:
- mermaid does not export `./package.json` in its exports map, so
require.resolve('mermaid/package.json') throws
ERR_PACKAGE_PATH_NOT_EXPORTED in runtimes that honor exports semantics.
The test now resolves the package entry and walks up to the package
root via a small findPackageJson helper.
- readFileSync from node:fs is replaced with `await Bun.file(...).text()`
to match the project's Bun-API requirement.
Validation:
- bun run typecheck (clean).
- bun test → 3996 pass / 0 fail across 305 test files.
Targets PRs:
- amDosion/claude-code-bast#8 (fork-internal review)
- claude-code-best/claude-code#386 (upstream review, same head branch)
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.
