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fix(preflight,server): stop reindex loop on Windows stdio MCP (#216) - #217
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…#216) Before: run_preflight quarantined chroma_db/ after a single non-zero probe exit. Any transient failure (lingering file lock from previous PID, cold GPU init, slow disk) triggered a destructive move and a full-corpus reindex. shutil.move's copy-tree fallback left partial copies AND a partially deleted live index when segment files were still open (WinError 32). subprocess.TimeoutExpired was uncaught and crashed main(). The [RECOVERY] log ran after the backup, so if backup itself crashed the original exit code was lost. After: - PROBE_ATTEMPTS=3 with PROBE_RETRY_DELAY_SECONDS=5 between tries; only quarantines after all attempts fail. - TimeoutExpired treated as inconclusive (keeps index). - os.rename (atomic on same volume) replaces shutil.move; on OSError the index is preserved and the process exits with EX_TEMPFAIL (75) instead of crashing halfway. - Every probe attempt appended to data/preflight.log so users can debug without depending on stdio-hidden stderr. Coverage: - test_transient_failure_recovers_on_retry - test_timeout_is_inconclusive_and_keeps_index - test_rename_failure_preserves_index_and_exits_75 - test_all_attempts_fail_calls_probe_three_times - existing test_probe_failure_backs_up_chroma_and_metadata now passes with PROBE_RETRY_DELAY_SECONDS monkeypatched to 0. Diagnosis and validated patch by @HillsCloud in the GH #216 comment thread.
Before: main() called orchestrator.index_all() synchronously before _run_transport(). On a 5000+ document corpus (~150k chunks, minutes) the MCP client timed out the `initialize` handshake, killed the process, restarted it against an empty index and looped indefinitely. The reporter observed tens of GB of auto-repair-* backups from the combined effect of this and the preflight bug fixed in 783b8e1. After: main() calls the existing start_reindex_background("incremental") (added in v4.3.0). The transport starts serving immediately and the client polls get_reindex_status for progress. Existing single-instance lock, watcher setup, and transport init are unchanged. Migration path (nuclear_rebuild after embedding-model change) is intentionally left synchronous to avoid returning query results with mixed embedding models. A follow-up will add a guarded async path with a "reindex in progress" error envelope. Regression coverage in tests/test_main_startup.py: - test_empty_collection_starts_background_not_sync — traps a future revert to index_all() sync. - test_populated_collection_triggers_no_indexing — neither path fires when count > 0. - test_start_reindex_background_returns_before_transport — records call order and asserts transport starts AFTER background init returns (the exact ordering the client depends on).
- CHANGELOG.md: Unreleased entries for fix(preflight) and fix(server) matching the two commits in this branch (783b8e1, b618e4d). - test-count-baseline.txt: 327 -> 334 (+7 new tests: 4 preflight, 3 main_startup). Bump reflects intent; the check is >=, so 811 currently collected keeps the gate green with room to spare.
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Navigate logical layers of code changes, visualize relationships, and explore their blast radius. 📝 WalkthroughWalkthroughPreflight retries failed probes, preserves the index after a timeout, and quarantines it only after three non-zero exits. Empty-collection startup now begins incremental indexing in the background before transport startup. ChangesStartup recovery and indexing
Priority: ➖ Normal Estimated code review effort: 3 (Moderate) | ~25 minutes Change: Bug fix · Severity of issue fixed: Medium Suggested reviewers: Merge Risk: 🟡 Moderate · up to A partial backup can leave the index empty on restart and prevent unchanged documents from being reindexed. Restore the original index when the second rename fails before merging. Security Architecture ReviewSecurity architecture risk: 🟡 Moderate · up to The server can now answer searches before its initial index is complete, so an empty result may mean “not indexed yet” rather than “not found.” The change does not show a new authentication bypass or expansion to another data store. Retained concerns
Security review detailsSecurity Blast Radius
Security Findings and Attack Paths
Trust Boundaries and Controls
Resilience and Maintainability Implications
Hardening Proposals
🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 70.83% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 24 functions across 4 files. (2 skipped: 2 unsupported.)
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Collapse two multi-line f-strings into single lines per ruff format's line-length judgment. Behavior unchanged; ruff format --check and ruff check both clean; 9/9 test_preflight + test_main_startup pass.
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- 🪄 Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at @mcp_server/preflight.py:
- Around line 57-62: Update the quarantine logic in run_preflight to roll back
the chroma_db rename if moving index_metadata.json fails with OSError. Track
whether chroma_db was moved, restore it to config.chroma_dir on failure, and
re-raise the error.
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.github/test-count-baseline.txtCHANGELOG.mdmcp_server/preflight.pymcp_server/server.pytests/test_main_startup.pytests/test_preflight.py
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| if config.chroma_dir.exists(): | ||
| shutil.move(str(config.chroma_dir), str(backup_dir / f"chroma_db.{reason}")) | ||
| os.rename(str(config.chroma_dir), str(backup_dir / f"chroma_db.{reason}")) | ||
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| metadata_file = config.data_dir / "index_metadata.json" | ||
| if metadata_file.exists(): | ||
| shutil.move(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json")) | ||
| os.rename(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json")) |
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🗄️ Data Integrity & Integration | 🟠 Major | ⚡ Quick win
The two-step quarantine can still leave a partial state.
os.rename is atomic only for each single item. If the chroma_db rename succeeds and the index_metadata.json rename then fails with OSError, run_preflight exits with code 75. At that point chroma_db is already in backups/ and the metadata is still live. On the next start, KnowledgeOrchestrator creates an empty collection and loads the stale index_metadata.json. index_all(force=False) then marks every unchanged file as skipped, so the index stays empty. The docstring on Line 106-109 promises that the index is "left untouched". Roll back the first rename when the second rename fails.
Proposed fix
- if config.chroma_dir.exists():
- os.rename(str(config.chroma_dir), str(backup_dir / f"chroma_db.{reason}"))
-
- metadata_file = config.data_dir / "index_metadata.json"
- if metadata_file.exists():
- os.rename(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json"))
+ chroma_dst = backup_dir / f"chroma_db.{reason}"
+ moved_chroma = False
+ if config.chroma_dir.exists():
+ os.rename(str(config.chroma_dir), str(chroma_dst))
+ moved_chroma = True
+
+ metadata_file = config.data_dir / "index_metadata.json"
+ if metadata_file.exists():
+ try:
+ os.rename(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json"))
+ except OSError:
+ if moved_chroma:
+ os.rename(str(chroma_dst), str(config.chroma_dir))
+ raise📝 Committable suggestion
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| if config.chroma_dir.exists(): | |
| shutil.move(str(config.chroma_dir), str(backup_dir / f"chroma_db.{reason}")) | |
| os.rename(str(config.chroma_dir), str(backup_dir / f"chroma_db.{reason}")) | |
| metadata_file = config.data_dir / "index_metadata.json" | |
| if metadata_file.exists(): | |
| shutil.move(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json")) | |
| os.rename(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json")) | |
| chroma_dst = backup_dir / f"chroma_db.{reason}" | |
| moved_chroma = False | |
| if config.chroma_dir.exists(): | |
| os.rename(str(config.chroma_dir), str(chroma_dst)) | |
| moved_chroma = True | |
| metadata_file = config.data_dir / "index_metadata.json" | |
| if metadata_file.exists(): | |
| try: | |
| os.rename(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json")) | |
| except OSError: | |
| if moved_chroma: | |
| os.rename(str(chroma_dst), str(config.chroma_dir)) | |
| raise |
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Review comment at @mcp_server/preflight.py around lines 57 - 62:
Update the quarantine logic in run_preflight to roll back the chroma_db rename
if moving index_metadata.json fails with OSError. Track whether chroma_db was
moved, restore it to config.chroma_dir on failure, and re-raise the error.
After applying the fix, consider running `coderabbit review --agent` for local
review. Visit https://docs.coderabbit.ai/cli?utm_source=ghpr
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| metadata_file = config.data_dir / "index_metadata.json" | ||
| if metadata_file.exists(): | ||
| shutil.move(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json")) | ||
| os.rename(str(metadata_file), str(backup_dir / f"index_metadata.{reason}.json")) |
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chroma_db succeeds but moving index_metadata.json fails, the server exits after the collection has already been moved. On restart, incremental indexing reads the stale metadata and skips unchanged documents, leaving their chunks missing from the fresh collection. Handle failure of the second move without leaving live metadata paired with an empty collection.
Prompt To Fix With AI
This is a comment left during a code review.
Path: mcp_server/preflight.py
Line: 62
Comment:
**Metadata can outlive its index** If moving `chroma_db` succeeds but moving `index_metadata.json` fails, the server exits after the collection has already been moved. On restart, incremental indexing reads the stale metadata and skips unchanged documents, leaving their chunks missing from the fresh collection. Handle failure of the second move without leaving live metadata paired with an empty collection.
---
For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.
| elif orchestrator.collection.count() == 0: | ||
| print("[INFO] No documents indexed. Running initial indexing...") | ||
| stats = orchestrator.index_all() | ||
| print(f"[INFO] Indexed {stats['indexed']} documents with {stats['chunks_added']} chunks") | ||
| # GH #216: initial indexing runs in a background thread so it | ||
| # does not block the MCP `initialize` handshake. Blocking here | ||
| # for a large corpus (~150k chunks takes minutes) caused stdio | ||
| # clients to timeout, kill the process, and restart into an | ||
| # empty index — an endless full-reindex loop. Users poll | ||
| # get_reindex_status() to track progress. | ||
| print("[INFO] No documents indexed. Starting initial indexing in background...") | ||
| orchestrator.start_reindex_background("incremental") |
There was a problem hiding this comment.
Prompt To Fix With AI
This is a comment left during a code review.
Path: mcp_server/server.py
Line: 4795-4803
Comment:
**Interrupted indexing never resumes** Initial indexing now writes to the live collection in a daemon thread. If the process exits after some documents are written but before indexing finishes, the next startup sees a nonempty collection and does not restart the job. The watcher does not scan on startup, so the remaining documents stay absent until someone requests another reindex.
---
For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.| # empty index — an endless full-reindex loop. Users poll | ||
| # get_reindex_status() to track progress. | ||
| print("[INFO] No documents indexed. Starting initial indexing in background...") | ||
| orchestrator.start_reindex_background("incremental") |
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search_knowledge can respond with "no_results" and “No relevant documents found,” even though the documents have not been indexed yet. Gate searches on initial-index readiness or include that state in the response.
Prompt To Fix With AI
This is a comment left during a code review.
Path: mcp_server/server.py
Line: 4803
Comment:
**Search hides indexing progress** The transport now accepts searches before initial indexing finishes. If a client searches while the collection is empty or only partly populated, `search_knowledge` can respond with `"no_results"` and “No relevant documents found,” even though the documents have not been indexed yet. Gate searches on initial-index readiness or include that state in the response.
---
For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.| return {"status": "started", "operation": mode} | ||
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| def track_transport(transport): | ||
| call_order.append(f"transport:{transport}") | ||
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| mock_orch.start_reindex_background.side_effect = track_background | ||
| monkeypatch.setattr(server, "get_orchestrator", lambda: mock_orch) | ||
| monkeypatch.setattr(server, "_run_transport", track_transport) |
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start_reindex_background with a function that returns immediately, so it checks call order without exercising the real thread launch. If that method later blocks until indexing completes, the test would still pass and miss the handshake regression it is meant to prevent. A controlled indexing worker would let the test verify that transport starts before indexing finishes.
Prompt To Fix With AI
This is a comment left during a code review.
Path: tests/test_main_startup.py
Line: 99-106
Comment:
**Handshake test masks blocking** This test replaces `start_reindex_background` with a function that returns immediately, so it checks call order without exercising the real thread launch. If that method later blocks until indexing completes, the test would still pass and miss the handshake regression it is meant to prevent. A controlled indexing worker would let the test verify that transport starts before indexing finishes.
---
For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!
Patch release: critical hotfix for #216 (Windows stdio reindex loop). Contains only the two fixes merged in #217 (783b8e1 preflight, b618e4d server), packaged as v4.9.1. Zero API changes, zero migration steps. - pyproject.toml: 4.9.0 -> 4.9.1 - mcp_server/__init__.py: __version__ -> 4.9.1 - npm/package.json: 4.9.0 -> 4.9.1 - CHANGELOG.md: promote Unreleased entries to v4.9.1 header Co-authored-by: Lyonzin <lyonzin@users.noreply.github.com>
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@lyonzin thank you so much for promptlly addressing this. Quick question - in order for it to work properly and not break it or cause issues with indexing, should I be running like this? Launch terminal and run "knowledge-rag" AND launching Claude with MCP configured should I just launch Claude ONLY that has the following MCP config and NOT launch terminal: should I launch knowledge-rag through terminal AND Claude with following config: |
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@HillsCloud — Option 2 is the correct one. Only Claude Desktop with the MCP config that includes Three reasons, all rooted in the diagnosis you did:
Recommended setup"knowledge-rag": {
"command": "c:\Knowledge-RAG\venv\Scripts\python.exe",
"args": ["-m", "mcp_server.server"],
"env": {
"KNOWLEDGE_RAG_SINGLE_INSTANCE": "1"
}
}Just this. No terminal. If you need CLI (init, backup, forced reindex)
DocsYou wrote in the original analysis:
You were right that the docs did not make this clear — that assumption was the doc's fault, not yours. I just opened #220 (docs-only, no code) that adds a "Who runs the server" section to |
…216 follow-up) (#219) * fix(preflight): rollback metadata rename when chroma_db move fails (#216) Follow-up to CodeRabbit + Greptile review on PR #217. The v4.9.1 _backup_active_index performed two sequential os.rename calls: chroma_db first, index_metadata.json second. If the second raised OSError (Windows antivirus scanning the JSON, brief file lock), the process exited with 75 while chroma_db was already in backups/ but metadata was still live. Restart then: 1. Probe reported "missing" (chroma_dir absent → SystemExit(0)) 2. main() saw collection.count() == 0 → dispatched background reindex 3. Orchestrator loaded orphan index_metadata.json → marked every doc as already indexed → skipped them all → empty collection, zero results, no error surfaced Fix: invert the order (metadata first — small file, low lock probability) and wrap chroma_db in try/except that rolls the metadata rename back on OSError before re-raising. Restart then sees the pristine pre-quarantine state and re-runs preflight cleanly. New test test_chroma_rename_failure_rolls_back_metadata mocks os.rename to succeed on metadata (call 1), fail on chroma_db (call 2), and asserts both files are back at their original paths after SystemExit(75). Locks rename call count at 3 (metadata-forward, chroma_db-forward-raises, metadata-rollback). * test(main_startup): assert main() completes under deadline with real thread (#216) Follow-up to Greptile PR #217 review finding P2. The v4.9.1 test_start_reindex_background_returns_before_transport mocked start_reindex_background with a lambda returning instantly, so a hypothetical refactor that collapsed the wrapper to synchronous would still pass the call-order assertion — main() would then block on the real work but the test would not catch it. Two hardening changes in this commit: 1. _mock_orchestrator_empty (shared helper used by every test in the file) now spawns a real 2 s daemon thread via _spawn_daemon_work whenever start_reindex_background is called. This matches the real v4.9.1 contract: return immediately, work happens in background. Every existing test in the file benefits. 2. New test_main_reaches_transport_under_deadline asserts main() completes in < 0.5 s. Combined with the realistic mock, this catches any regression where start_reindex_background becomes synchronous — main() would then await the daemon's 2 s work and the timing assertion would fail (elapsed >= 2.0 > 0.5). * chore: CHANGELOG + test-count baseline for #216 follow-up fixes - CHANGELOG.md: Unreleased entries for fix(preflight) and test(main_startup) matching the two commits in this branch. - test-count-baseline.txt: 334 -> 336 (+2 tests: test_chroma_rename_failure_rolls_back_metadata, test_main_reaches_transport_under_deadline). --------- Co-authored-by: Lyonzin <lyonzin@users.noreply.github.com>
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@lyonzin thanks for such a detailed reply. The issue I am having is that when I have this the config that you recommended, i.e., the below one: "knowledge-rag": { I have this and do not run terminal but despite that Claude Desktop repeatedly complains that MCP knowledge-rag: server disconnected error: 
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For some reason, i continue to have issues with the knowledge-rag MCP. I understand terminal should not be used with Claude at the same time. Does this mean that knowledge-rag MCP cannot be used with LM Studio, Claude, and Codex at the same time? In other words, only Claude MCP be used and if i were to use knowledge-rag MCP through LM Studio, then I have to close Claude first? |
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@HillsCloud correction on my earlier reply about multi-client v4.0+ already supports multi-client. Just switch the transport.
Setup
Trade-offs vs stdio
This unblocks your three-client setup today, without waiting for #34. For the "server disconnected error" — I still need the data I asked for earlier ( I'll open a docs issue to make the HTTP transport path discoverable — this should have been one of the first things the README surfaced. |
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Thanks @lyonzin for clarifying in depth. I am not a developer but know just barely enough. It looks like even though I just run Claude Desktop, somehow cowork and code also tries to start the mcp process causing it to display multiple errors (disconnected or couldn't start, etc) when Claude Desktop is opened. I see 4 processes spawning even though I am just running Claude Desktop. This leads to Claude getting inconsistent/unstable MCP connection with knowledge-rag. I would like to get the flexibility of using it with ChatGPT Desktop and Claude as welll as others. Update: I tried the streamable option and it's working. I do have to launch the process separately now as opposed to previously launching Claude alone. No more errors now. Thanks!! Future Feature request: Some sort of small windows GUI interface would be very helpful in launching Knowledge-rag and showing the indexing status along with ability to include/exclude folders (perhaps something similar to LocalSynapse). |
Summary
Fixes the endless full-reindex loop that #216 documented on Windows stdio MCP clients. The bug was the interaction of three problems:
main()ran initial indexing synchronously and blocked the MCPinitializehandshake past client timeout;run_preflightquarantined the whole index after a single transient failure; andshutil.move's copy-tree fallback corrupted the live index while creating a partial backup when segment files were still held open by a lingering PID.Closes #216
Type of change
What changed
mcp_server/preflight.py(rewrite): retryPROBE_ATTEMPTS=3×PROBE_RETRY_DELAY_SECONDS=5;subprocess.TimeoutExpiredtreated as inconclusive (index preserved);os.renamereplacesshutil.move(atomic on same volume, no partial-copy fallback);SystemExit(75)onOSErrorduring rename instead of crashing halfway; every attempt appended todata/preflight.logfor post-mortem when stdio hides stderr.mcp_server/server.py(lines 4795–4803):main()now callsorchestrator.start_reindex_background(\"incremental\")instead oforchestrator.index_all()sync for empty collections. Migration path (nuclear_rebuildafter embedding-model change) intentionally kept synchronous — follow-up issue will add guarded async path.tests/test_preflight.py(+4 tests): transient recovery, timeout inconclusive, rename-failure exit code,PROBE_ATTEMPTScount guard. Existing test monkeypatchesPROBE_RETRY_DELAY_SECONDS=0to keep runtime flat.tests/test_main_startup.py(new, +3 tests): trap future regressions that swapstart_reindex_backgroundback for a synchronous call; assert transport starts BEFORE background init completes.CHANGELOG.md: Unreleased entries for bothfix(preflight)andfix(server)..github/test-count-baseline.txt: 327 → 334 (+7 tests).Why
@HillsCloud reproduced the loop on a ~5000-doc / ~150k-chunk corpus, captured
link_lists.bincorruption on the persisted HNSW segment, and validated the exact patch shape below on their environment before commenting. The root causes are three independent bugs inmain()andpreflight.py— this PR fixes the two that turn a single bad segment into an infinite full-reindex. The third (single-instance guard opt-in) is left for a follow-up because flipping it default-on is a breaking change (LEI 1 backwards-compat).7 Pillars Quality Gate
1. Security
eval/exec/subprocess shell=True/pickle.loads. The existingsubprocess.run([sys.executable, \"-c\", code], ...)in_probe_chromais unchanged.2. Stability
PROBE_RETRY_DELAY_SECONDSmonkeypatched to 0 in every retry test; notime.sleepin test bodies; no network3. Memory leak
preflight.logusesopen(..., \"a\").with— no lingering file handlesdaemon=Trueand reuses the existing_reindex_progressstate guard added in v4.3.04. Versatility
os.renamerequires same-volume for atomicity — verified:config.chroma_dirandbackup_dirare both underconfig.data_dirpathlib.Path+encoding=\"utf-8\"used throughoutX | Nonefrom__future__ annotations)5. Scalability
index_all()took (minutes → milliseconds)start_reindex_backgroundalready carries the_reindex_progress[\"active\"]guard added in v4.3.0; watcher will not double-triggerPerformance impact:
The extra probe attempts add wall-clock ONLY on the failure path — the healthy startup does exactly one probe as before.
6. Versioning
run_preflight()andmain()signatures unchanged;PROBE_ATTEMPTS/PROBE_RETRY_DELAY_SECONDS/PROBE_TIMEOUT_SECONDSare new module constants (not API)## Unreleasedscripts/check_api_surface.py --checkreports[OK] No breaking changes to public API surface.7. Quality
ruff check/ruff format— will be verified by CI (Python 3.14 local is one version ahead of the matrix's 3.13; ruff runs on all matrix cells)_log,_backup_active_index,_probe_chroma,run_preflightrun_preflighthas one for-loop, one try/except, ≤ CC-BMigration / Breaking changes
N/A
Test plan
pytest tests/test_preflight.py tests/test_main_startup.py -x→ 9 passedpytest -xfull suite → 811 passed, 1 skipped, 8 xfailedpython scripts/check_version_sync.py→ OK (no bumps in this PR)python scripts/check_api_surface.py --check→ OKDocumentation
CHANGELOG.mdupdatedREADME.mdunchanged (no user-facing config surface added)docs/unchanged (docs/single-instance.mdfollow-up will get the terminal-vs-MCP guidance the reporter suggested)Release plan (post-merge)
Ship as v4.9.1 (patch — bug fix, zero API changes). Follow-up issues to open after merge:
nuclear_rebuild(currently sync — safe but blocking on embedding-model change)KNOWLEDGE_RAG_SINGLE_INSTANCE=1default-on for writers (breaking, needs semver discussion)docs/single-instance.mdclarifying stdio-MCP-client-managed lifecycleSummary by CodeRabbit
Bug Fixes
Tests
This PR is not yet safe to merge because interrupted indexing and a partial quarantine can leave documents silently absent.
Fix with agent prompt
Summary
The PR retries Chroma startup probes, treats probe timeouts as inconclusive, replaces backup copy fallback with renames, and moves initial indexing behind MCP startup. The review found that:
Diagram
%%{init: {'theme': 'neutral'}}%% flowchart TD A[Startup preflight] --> B{Probe succeeds?} B -- No, after retries --> C[Rename collection, then metadata] C --> D{Metadata rename fails?} D -- Yes --> E[Exit with stale live metadata] E --> F[Restart: empty collection skips unchanged documents] B -- Yes --> G[Open collection] G --> H{Collection count is zero?} H -- Yes --> I[Start background incremental index] I --> J[MCP transport starts] I --> K{Process exits mid-index?} K -- Yes --> L[Restart sees partial, nonempty collection] L --> M[Initial index is not resumed]Reviews (1) · Last reviewed commit: "chore(format): apply ruff format to pref..."