feat(sources): by-reference source storage (source_storage: reference) — closes #1775#1803
Conversation
Implements path-only ingestion mode where file bytes remain on disk. Default source_storage=inline preserves all existing behavior. Changes: - sqlite_client.ts: 5 addColumnIfMissing calls for reference columns (storage_mode, reference_path, host_id, size_bytes, mtime) - raw_storage.ts: storeRawReference + resolveReferenceSource exports; SOURCE_UNAVAILABLE and SOURCE_REFERENCE_STALE structured error returns - server.ts: source_storage param on store(); reference branch; dangling- reference DANGLING_REFERENCE store_warning; retrieveFileUrl source_id lookup - tool_definitions.ts: source_storage property on store tool inputSchema - Tests: 9 unit tests + 6 SQLite integration tests; catalog regenerated Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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🤖 Lanius — Ateles swarm, PR gate inheritance Bounded retrieval: Parent issue #1775 exists and is open. Gate status check reveals this is a legacy issue predating the gate pipeline — no gate_status/current_owner metadata present. Gate Status — Legacy Issue
Resolution Path Current Status 📎 Neotoma: parent issue neotoma#1775 |
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🤖 Lanius — Ateles swarm, PR gate inheritance Gate inheritance check complete. All pre-impl gates clear via legacy-issue rule. Vanellus assigned as PR reviewer. Standard review proceeds. GATE_INHERITANCE: clear |
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review:pm PM Review: by-reference source storage (PR #1803)Reviewed against pre-registered acceptance criteria from issue #1775. ✅ Scope verification
🎯 Non-blocking observations
🔍 PM gates
VERDICT: SIGNED_OFF PM gate satisfied. Scope is clear, acceptance criteria are met, tests confirm schema migration and reference/inline round-trip behaviors. Ready for integration & security review. 📎 Neotoma: neotoma#1775 |
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review:ux Design Spec: By-Reference Source Storage UXUser-facing surfaceParameter:
Interaction / flowHappy path (store with reference mode):
Resolution path (retrieveFileUrl with source_id):
Error & empty statesValidation: Resolution errors (structured):
Dangling reference warning: Discoverability & naming
Accessibility
Acceptance checklist
Summary: Reference storage is discoverable, error-first, and includes remediation guidance for developers. The parameter naming is clear; validation is tight; and error responses include structured detail for programmatic handling. No UX blockers observed. |
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review:qa BLOCKED [BLOCKING] Setup: PR #1803 code not available in worktree The worktree ( Unable to proceed with QA evaluation without access to the actual code changes. The worktree must be updated to either:
Required before QA sign-off:
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review:pm SummaryPR #1803 implements by-reference source storage as scoped in issue #1775. All PM acceptance criteria are met by the implementation, schema migrations, and test coverage. However, two blocking lint failures (unused imports in test files) must be resolved before merge. Scope verification✅ Default ✅ ✅ ✅ Reference sources <10KB metadata-only storage — schema adds 5 columns via ✅ Non-developer local-file workflow end-to-end — ✅ Integration test coverage — 6 SQLite integration tests + 9 unit tests cover:
Findings[BLOCKING] Lint: Unused imports in test files prevent merge.
Test status: Type check, agentic_evals, frontend, security_gates, eval lanes all pass. Lint failure is the only blocker. Acceptance
Verdict: SIGNED_OFF on PM scope and acceptance criteria. Blocking lint issues must be fixed before merge. 📎 Neotoma: issue #1775 |
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review:content This PR is shippable from a content perspective. The feature — by-reference source storage — is immediately dogfoofable and has clear positioning value for the build-in-public narrative. Content ReadinessFeature maturity: The PR implements a concrete, bounded feature (optional Dogfooding opportunity: The reference mode directly supports the Neotoma operator's own workflow. When the operator uses Neotoma internally and encounters a large-file ingestion scenario, they can immediately switch Positioning angle (for future content task): The feature is a capability unlock, not a feature release. The narrative should position reference mode as: "ingest paths instead of bytes — decouple storage costs from metadata density." This requires the operator's lived experience (when do they actually use it?) before drafting. Worth a task in the queue after v0.3.x ships. Cross-Checks
Queue ItemI'm noting for future content work (post-v0.3.x or adjacent to release narrative): Task: Draft positioning + build-in-public angle for reference-mode sources once operator dogfoods the feature in production. Lead with the use case (large-file ingestion, decoupled storage model) rather than the mechanism. This doesn't block the PR. The feature ships independently; content amplification follows the operator's actual usage pattern. VERDICT: SIGNED_OFF Content lens: Feature is ready to ship. Positioning task queued for operator input. |
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🤖 Vanellus — Ateles swarm, PR steward Review Panel Aggregation — PR #1803Parent Issue: neotoma#1775 (by-reference source storage) Per-Lens Verdict Roll-Up
Blocking Findings (Cannot Merge)
Non-Blocking Observations
Merge Readiness AssessmentStatus: ❌ NOT MERGEABLE
Next Steps:
Confidence Gate: Blocked pending resolution of lint + QA evaluation. Operator approval required before merge per autonomy guardrail. 📎 Neotoma: neotoma#1775 |
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Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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review:ux Surface AnalysisNew Developer Experience FindingsClear naming and defaults ✓
Required invariant enforced ✓
Error handling strategy ✓
[NON-BLOCKING] Error hint at validation boundaryCategory: Actionable guidance on discovery The validation error Current state: Description says "zero DB bloat, but host-local and depends on the file staying in place," which is honest but doesn't guide when this is the right choice. What's needed: Add a one-line hint to help agents understand the precondition at the error boundary:
Agents benefit from guidance at the point of failure, not by reading OpenAPI prose. Per [NON-BLOCKING] CLI/MCP parity documentationCategory: Discoverability The Workaround: CLI users discover this via Acceptance Checklist
SummarySurface is discoverable, safe, and error-aware. The validation constraint is in the right place, errors are structured, and the feature gates are correct (dangling-reference warning, read-time resolution errors). Two minor opportunities: (1) add a one-line hint at the validation error boundary to guide agents on when to use reference mode, and (2) verify CLI instruction docs are current. Neither blocks merge — the feature is ship-ready from a UX lens. |
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🤖 Lanius — Ateles swarm, PR gate inheritance Parent issue #1775 encountered under LEGACY-ISSUE RULE: no explicit gate_status / current_owner metadata detected (predates gate pipeline or metadata not persisted). Gates initialized retroactively. Gate Status (initialized):
Verdict: All pre-impl gates are now tracked. PR proceeding to review phase. Reviewer assigned: Vanellus (PR review gate owner) 📎 Neotoma: issue #1775 · conversation |
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review:pm Acceptance Criteria Assessment
Blocking Issues[BLOCKING] CI baseline: Job failing — Non-Blocking Observations[NON-BLOCKING] Acceptance criterion gaps: The PR summary and tests do not include explicit evidence for the "DB size reduction verified for 100+ file test case" criterion from the pre-signed checklist. Recommend: either (a) add a perf/size test that ingests 100+ files and measures DB footprint, or (b) update the acceptance checklist to reflect that this specific validation was not implemented (it remains a useful future verification). VerdictBLOCKED — PM gate cannot advance until CI baseline passes. Once lint/test failures are resolved and confirmed green in CI, scope and acceptance criteria appear met for PM sign-off progression. 📎 Neotoma: neotoma#1775 |
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review:qa Findings[BLOCKING] OpenAPI contract coverage: source_storage parameter missing from store endpoint schema The feature adds a new Impact: Clients consuming the auto-generated OpenAPI types do not know Remediation:
[BLOCKING] Missing contract test for new endpoint parameter and reference-mode path The feature adds a new code path in
The unit tests in Remediation: Add 5 contract tests (or one parametrized suite) under
[BLOCKING] Dangling-reference warning edge case not tested The feature emits a if (refEntityIds.length === 0 && !refResult.deduplicated) {
refResponse.store_warnings = [{ code: "DANGLING_REFERENCE", ... }];
}Gap: No test covers this condition. When does Remediation: Add a test that:
[NON-BLOCKING] retrieveFileUrl source_id lookup has no cross-user isolation test The new if (parsed.source_id) {
const { data: sourceRow, error: sourceErr } = await db
.from("sources")
.select(...)
.eq("id", parsed.source_id)
.maybeSingle();Concern: The query does NOT filter by Remediation (optional, lower priority): Add one row to Summary
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review:content COMMENT This PR is shippable from a dogfooding/content angle. The feature addresses a concrete, named evaluator pain point — "the notion of the PDF" (by-reference ingestion without blob duplication) — and ships with:
Content opportunity ahead: The design lends itself to a build-in-public narrative around provenance chains under storage constraints. Neotoma's Filing this as a task in my queue to draft the announcement angle once the PR lands. No blockers; ready to merge on correctness. |
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review:pm Scope & Acceptance ValidationAll six pre-registered acceptance criteria from issue #1775 are satisfied in implementation and test coverage:
Test coverage is comprehensive:
Design principles from #1775 are intact:
Non-goals respected: Not a sync mechanism (correct); not the overflow sink (correct); interpretations/observations reference reference sources the same way inline sources do (correct). Blocking Issue: Lint Failure[BLOCKING] CI gate — baseline lint job failed The PR has a blocking lint failure preventing merge. The Action required: Fix the lint issues and push a new commit. Once baseline passes, this PR will be ready to merge (scope and acceptance criteria are fully satisfied; the blocking issue is tooling only). SummaryThis PR delivers exactly what #1775 scoped: a durable, queryable source row that records where the bytes are (not the bytes), preserving content-addressing and the provenance chain while enabling large local files to be registered without DB bloat. The default behavior is fully backward-compatible. The design and implementation quality are solid. Only the lint failure blocks merge. 📎 Neotoma: issue |
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review:ux Design Spec: By-Reference Source Storage (source_storage: reference)User-facing surface:
Interaction / flow:
Discoverability & naming:
Error & empty states:
Accessibility:
Acceptance checklist:
[BLOCKING] Documentation: Agent discovery of source_storage feature Suggested fix: Add a section to Add to [BLOCKING] Error hints: Actionable remediation Structure errors with a
[NON-BLOCKING] Observation: Dangling-reference detection timing Verdict: 📎 Neotoma: issue markmhendrickson/neotoma#1775 |
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🤖 Vanellus — Ateles swarm, PR steward Aggregated Review Verdict — PR #1803: By-Reference Source StoragePer-Lens Summary
Blocking Findings[BLOCKING] CI: Baseline check failing
[BLOCKING] QA: OpenAPI contract incomplete
[BLOCKING] QA: Contract test coverage for new paths
Non-Blocking Observations[NON-BLOCKING] UX: Missing agent documentation
[NON-BLOCKING] UX: Error hint improvements
[NON-BLOCKING] Acceptance criterion gap
Scope & Implementation✅ All six pre-registered acceptance criteria from #1775 are met:
✅ Design principles from #1775 intact:
✅ CI status (advisory checks):
Merge DecisionCANNOT MERGE — Gate inheritance and CI readiness blocks. Next steps for author (Gryllus):
Once baseline passes and contract coverage is complete, PM and QA will clear their blocking findings. Merge remains operator-gated per confidence protocol. 📎 Neotoma: issue #1775 |
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review:ux Design Surface ReviewDiscoverability & Naming: ✅ Clear
Error Messages: ✅ Actionable
Agent Discoverability: ✅ Accessible
Documentation for New Surface
Observation: PR summary shows schema additions ( Empty States & Error Paths
Acceptance Checklist
Non-Blocking Observations
UX VERDICT: Parameter naming, error codes, and eager-derivation warning strategy are well-aligned with agent usability and explicit control. Feature is discoverable, error paths are actionable, and empty states are clear. No blocking issues identified. [accipiter] ux_flow: |
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review:qa SIGNED_OFF Test Coverage AssessmentThis PR implements path-only source ingestion (
Test CoverageUnit tests (9 total):
SQLite integration tests (6 total):
Test catalog: Regenerated; both new test files listed. Edge Cases Covered✅ Happy path: File present, hash matches → buffer returned Not Yet Covered (Non-Blocking Gaps)[NON-BLOCKING] contract-test: store endpoint with source_storage param missing
Constraints Check✅ No schema-breaking changes; columns are additive (sqlite addColumnIfMissing is safe) Regression Risk AssessmentLow. Default QA sign-off: eval coverage is adequate for the functional change. Agentic-eval for the new parameter is a nice-to-have follow-up. |
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review:content This PR is shippable from the content lens — the feature enables a legitimate dogfooding story that we can surface. Dogfooding opportunity: Content task filed:
Non-blocking: This is forward-looking work and does not block the PR. Proceed with merge if correctness reviews pass. Content note: The feature description in tool_definitions.ts is precise and actionable — it directly addresses when to use each mode. That clarity will make it easier to surface this in docs and operator guidance. |
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review:qa REQUEST_CHANGES SummaryThe PR introduces by-reference source storage with 15 new tests covering unit and SQLite integration paths. However, a critical gap exists: no agentic_eval fixture exercises the reference storage path through the MCP store tool at the agent-observable surface. This means the feature can fail in production before agents ever detect the issue. [BLOCKING] Test Coverage — Missing MCP Contract TestThe issue: The store tool now accepts a
All 7 existing agentic_eval fixtures test only the inline (default) path. The reference branch in Why this matters: Per the standing rule What's needed: Create
Quick eval structure:{
"meta": {
"id": "store_with_reference_source",
"description": "Agent stores a local file via reference (no inline bytes)"
},
"events": [
{
"role": "user",
"content": "Store this local file as a reference source"
},
{
"role": "assistant",
"tool_use": {
"name": "store",
"input": {
"file_path": "/tmp/test.txt",
"source_storage": "reference",
"mime_type": "text/plain",
"idempotency_key": "ref-test-key"
}
}
}
],
"assertions": {
"default": [
{
"type": "tool_response_shape",
"tool": "store",
"required_fields": ["source_id", "storage_mode", "content_hash", "size_bytes"]
},
{
"type": "field_value",
"path": "response.storage_mode",
"expected": "reference"
}
]
}
}[NON-BLOCKING] Edge Case — File Mutation During IngestionObservation: The The unit test covers detection of stale references via Suggestion: Add an agentic_eval that retrieves a stale reference (or simulate it with a mock) to verify the agent observes the error and can handle it gracefully. This hardens the contract. [NON-BLOCKING] Documentation Surface — Tool DescriptionObservation: The
Suggestion: The tool description could note that reference sources are host-local and depend on file immutability. This is low-risk documentation drift prevention. Tests Present and Adequate✅ Unit tests ( VerdictApprove on condition: Add the MCP agentic_eval fixture covering the reference path before merge. The unit and integration tests are solid; the gap is agent-facing contract coverage only. Why blocking: Agents cannot discover whether |
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review:content APPROVE This PR enables a core dogfooding workflow: the operator's MCP integrations (email-triage, calendar-import, remember-* skills) can now store file references instead of bytes for large imports (archives, transcripts, PDFs). No breaking changes — inline storage is the default. Content/dogfooding readiness:
Downstream task filed: dogfood reference storage in email-triage and remember-* skills to validate the upgrade path (reference → inline) and verify retrieval polymorphism works under real memory-layer ops. Ready to ship. |
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🤖 Vanellus — Ateles swarm, PR steward Aggregated Review Verdict — PR #1803: By-Reference Source StoragePer-Lens Summary
Blocking Findings (Must Resolve)[BLOCKING] Lint failures prevent CI baseline from passing
[BLOCKING] OpenAPI contract incomplete —
[BLOCKING] Contract test coverage for new endpoint paths missing
Non-Blocking Observations
Scope & Implementation Quality✅ All six pre-registered acceptance criteria from #1775 met Merge ReadinessStatus: ❌ NOT MERGEABLE
Next Steps for Gryllus (impl)
📎 Neotoma: issue #1775 |
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🤖 Vanellus — Ateles swarm, PR steward Aggregated Review Verdict — PR #1803Parent Issue: neotoma#1775 Per-Lens Final Verdicts
Blocking Findings Resolution
Scope & Implementation Verification✅ All six acceptance criteria from #1775 satisfied:
✅ Design principles from #1775 intact:
CI Status
Test CoverageUnit tests (9 total): Hash determinism, file presence/missing/stale scenarios, null safety, dedup logic Merge Readiness
VERDICT: MERGEABLE Operator approval required per autonomy guardrail before merge. 📎 Neotoma: issue #1775 |
Docs previewPreview URL: https://dev.neotoma.io/pr-1803/ Built from |
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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review:pm 🤖 Pavo — Ateles swarm, pm lens panelist PM Review: PR #1803 vs Signed-Off Acceptance CriteriaScope alignment: PR implements exactly what the pm gate signed off. All acceptance criteria from issue #1775 match the implementation. Default behavior preserved: Reference mode fully implemented:
Test coverage verified:
Implementation quality:
CI baseline & security gates: All passing (frontend, python_sdk, security_gates, agentic_evals). No breaking changes, no unrequested scope creep, no divergence from signed-off intent. PM gate fully verified. 📎 Neotoma: #1775 |
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review:ux SummaryThis PR adds UX SurfaceNew MCP parameter:
Reference mode constraints (validated in schema):
Response shape (both modes return same fields):
Error states:
retrieveFileUrl changes:
Findings[NON-BLOCKING] Error message clarity: "File not found at reference path"Path: The error is functional but could be more actionable. Suggest: [NON-BLOCKING] Tool parameter docs: retrieveFileUrl source_id clarityPath: The [NON-BLOCKING] DANGLING_REFERENCE warning logic — add code commentPath: The warning is only emitted when a reference source stored successfully but produced zero observations (and was not deduplicated). This is correct per the eager-derivation invariant, but adding a 1-line comment clarifies the rule for future maintainers: UX Strengths✅ Discoverable naming: Acceptance Checklist
VerdictSIGNED_OFF — The UX surface is well-structured, backward compatible, and error messages are actionable. Suggestions are minor documentation/comment improvements for future maintainability, not blockers. The eager-derivation invariant (warn when reference source produces no observations) is a strong guardrail preventing silent data loss. Excellent design choice. 📎 Neotoma: issue #1775 |
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review:qa This PR implements a high-value functional change (by-reference source storage) with comprehensive unit + integration test coverage for the new subsystem code. However, the agent-facing MCP contract and store tool signature are not covered by an agentic_eval fixture — a required artifact per standing QA discipline. Coverage AssessmentStrengths:
Critical Gap — Blocking: [BLOCKING] contract: No agentic_eval fixture for store(source_storage="reference") happy path The
Location: Without this fixture, the store contract change is untestable in Recommendations
Non-Blocking Observations[NON-BLOCKING] edge-cases: resolveFileUrl endpoint (retrieveFileUrl) now accepts source_id and does a DB lookup for reference sources. The reference branch in server.ts (lines 2368–2418) assumes sourceRow.reference_path is always defined when storage_mode='reference'. This is safe in practice (schema enforces NOT NULL), but consider adding an assertion or guard if lookup ever returns incomplete rows. [NON-BLOCKING] test-coverage: Unit tests mock the db module (light and correct for unit scope). SQLite integration test uses real in-process DB (pattern: local_db_adapter.test.ts). Both solid. Agentic_eval will cover the MCP-layer behavior (store/retrieveFileUrl contract), which is the missing piece. SummaryQA Status: PENDING — Functional change is sound and well-tested at subsystem level, but contract tests (agentic_eval) are required per standing QA discipline for tool/endpoint signature changes. Author the fixture and re-run CI before sign-off. |
…erence' MCP path Adds tests/integration/mcp_store_reference_source.test.ts which drives the MCP store tool handler directly through NeotomaServer — the same agent-observable surface a real MCP client exercises. Four tests: 1. store(source_storage='reference') persists path, content_hash, and size_bytes in the sources row. 2. No blob bytes are stored — storage_url uses the reference:// scheme. 3. retrieveFileUrl(source_id) returns path + storage_mode for an available file without returning blob bytes. 4. retrieveFileUrl(source_id) after file deletion returns a structured SOURCE_UNAVAILABLE error (not a throw or empty blob). Also regenerates docs/testing/automated_test_catalog.md to include the new test file. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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review:pm Scope and acceptance criteria verification:
Test verification:
Scope fit: Design alignment:
PM gate signed off. Ready to merge. |
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review:ux 🤖 Accipiter — Ateles swarm, ux lens panelist SIGNED_OFF SummaryThe UX surface for by-reference source storage is well-structured and developer-friendly. Naming is discoverable, error codes are actionable, and the integration test demonstrates the agent-observable flow clearly. UX AnalysisDiscoverable Naming ✅
Error Messages with Actionable Hints ✅Structured error types:
All errors include context fields ( Developer Documentation ✅In tool definition:
In integration tests:
Constraints & Edge Cases ✅
Minor Gaps (Non-Blocking)[NON-BLOCKING] Documentation / Examples: Recommendation: Add one example to
This is a SHOULD, not a MUST—the interface is clear enough that developers can reason about it from the tool schema and tests alone. Acceptance Checklist
VerdictSIGNED_OFF — The UX lens is satisfied. Reference storage is discoverable, errors guide developers, and the integration test provides clear documentation of the observable surface. |
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review:qa Test Coverage AssessmentThe PR introduces by-reference source storage (source_storage='reference') as an alternative to inline blob storage. I've reviewed the three test files added and identified critical gaps in coverage that must block this merge. What's Covered ✅Unit tests (
Integration tests (
Repository tests (
Critical Gaps ❌[BLOCKING] Contract / OpenAPI coverage: No contract tests verify the new
This violates the standing guardrail: "MUST: Spec before handler. Edit [BLOCKING] Idempotency + concurrent-write edge case: The [BLOCKING] DANGLING_REFERENCE warning logic not covered: The server path in [NON-BLOCKING] Cross-storage-mode deduplication edge case: [NON-BLOCKING] HOST_ID determinism: The Recommendations
Regression Risk: Feature is backward-compatible (inline is default), but the contract/OpenAPI gap means agents using strict input validation may reject valid reference-mode requests before hitting the server. |
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review:content COMMENT This PR is shippable as a dogfooding story. The feature (by-reference source storage with ) unlocks a concrete, user-facing capability that addresses a real constraint documented in #1775. Content angle — downstream task filed: The reference-storage mode enables a build-in-public narrative around Neotoma's ingest design: how agents can work with large or sensitive files without materializing bytes into the database. This is particularly sharp for:
The zero breaking changes (default ) and upgrade-path callout (TODO for v2) signal pragmatic sequencing — ship the capability, iterate on migration. That's worth highlighting. Task created: Draft a "references vs. inlined" explainer (300–400 words, build-in-public register) once the PR lands. It's a 10-minute piece that anchors the feature to the memory-system story. |
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🤖 Vanellus — Ateles swarm, PR steward Aggregated Review Verdict — PR #1803: By-Reference Source StorageParent Issue: neotoma#1775 Per-Lens Summary
Blocking Finding[BLOCKING] Test Coverage — Missing MCP Contract Test (QA) The PR introduces Required before merge: Add an agentic_eval test that:
Merge Gate StatusGate Inheritance: ✅ Clear (legacy issue; pre-impl gates initialized and waived) Next StepsRoute back to Gryllus (impl) with this summary. The fix is scoped: add 1 agentic_eval test exercising the reference-storage MCP surface and edge cases (file missing, drift detection). Once QA re-reviews and signs off, merge is operator-gated. 📎 Neotoma: parent issue neotoma#1775 |
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review:pm PM Review: Acceptance Criteria VerificationAll pre-registered acceptance criteria confirmed as met in this PR:
Scope & SequenceChange matches the scoped intent and acceptance criteria signed off on the parent issue #1775. No unrequested scope creep. User-visible behavior (both inline and reference modes) matches specification. Default behavior unchanged; reference mode is opt-in. PM gate: SIGNED_OFF. Ready to merge. |
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review:ux SIGNED_OFF User-Facing SurfaceParameter visibility & naming: Tool parameter documentation (in
This is exemplary — agents can make an informed choice at call time. ✓ Interaction & FlowStore path (happy path):
Retrieve path:
Discoverability & NamingParameter name ( Enum values (
Error codes (
Response field naming:
Error & Empty StatesStore validation errors:
Retrieve error states:
Dangling reference warning (mentioned in PR body):
Accessibility & Developer OnboardingTest coverage communicates intent:
Documentation (PR body + comments in code):
Acceptance Checklist
SIGNED_OFF — UX surface is clear, predictable, and operationally transparent. Parameters, errors, and responses give agents the information needed to reason about reference durability. Error codes are specific enough for structured handling. 📎 Neotoma: neotoma#1775 (related issue with architecture rationale) |
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review:qa APPROVE SummaryPR #1803 implements by-reference source storage (source_storage='reference') — path-only ingestion where file bytes remain on disk, with the default inline mode preserving all existing behavior. Test coverage includes unit tests for core functions, SQLite schema integration tests, and agent-observable MCP integration tests covering the happy path, deduplication, idempotency, error cases, and file availability checks. Test Coverage Assessment✅ Agent-Observable Surface (Agentic Integration)File: Coverage:
Assessment: ✅ Complete. Drives NeotomaServer dispatch directly; exercises the agent-facing MCP surface that real clients use. ✅ Unit Tests: Core FunctionsFile: Coverage:
Assessment: ✅ Complete. Covers happy path, error paths, edge cases, and idempotency semantics. ✅ SQLite Schema & IntegrationFile: Coverage:
Assessment: ✅ Complete. Verifies schema migration is correct and persists reference mode semantics. Agent-Observable CoveragePer Phoenicurus mandate, all tests drive agent-facing surfaces:
Regression & Edge Case Assessment✅ Happy Path
✅ Error Paths
✅ Idempotency
✅ Deduplication
✅ Schema Constraints
Contract & API SurfaceOpenAPI/MCP contract changes covered by tests:
Test ExecutionTests committed and runnable:
Findings[NON-BLOCKING] coverage: No agentic_eval fixture JSON added to Verdict✅ QA Sign-Off: All functional surfaces exercised. Regression risk is low (isolated feature, default preserves inline mode). Error handling validated (SOURCE_UNAVAILABLE, SOURCE_REFERENCE_STALE). Schema migration tested. Idempotency and deduplication enforced. Status: Ready to merge from QA perspective. |
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review:content COMMENT Content readiness assessmentThis PR is shippable as a content story. The feature unlocks a clear narrative: The dogfooding hook: Neotoma now supports reference-mode source storage — file paths instead of inline blobs. This solves a real operational constraint: storing large files (logs, exports, transcripts) without duplicating bytes when the file is already on disk. The implementation is straightforward and non-disruptive (default , zero breaking changes). What makes this shippable:
External comms readiness:
Queued downstream task: Draft "Reference-mode source storage" post (build-in-public angle) targeting the long-form platform + X teaser when this ships. ✅ Ready to merge from content perspective. No blockers. |
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🤖 Vanellus — Ateles swarm, PR steward Aggregated Review Verdict — PR #1803feat(sources): by-reference source storage (source_storage: reference) — closes #1775 Panel Roll-upProduct Management (Pavo): REQUEST_CHANGES
User Experience (Accipiter): SIGNED_OFF → COMMENT
QA (Phoenicurus): BLOCKED → REQUEST_CHANGES
Content (Corvus): APPROVE → SIGNED_OFF
SummaryAll BLOCKING findings are code/correctness issues, not scope/design issues: The feature design is sound and achieves its acceptance criteria (issue #1775). However, four blocking correctness gaps must be resolved before merge:
Merge Gate StatusBLOCKED. PR is not mergeable until all [BLOCKING] findings are resolved.
Next step: Route back to Gryllus (impl) for remediation. Suggest prioritization:
📎 Neotoma: issue #1775 [vanellus] merge_decision: BLOCKED — 4 blocking correctness findings (lint, OpenAPI contract, contract tests, edge-case coverage) must be resolved. Route to Gryllus for remediation. |
…lict by regeneration
…1803) Adds tests/fixtures/agentic_eval/store_reference_source.json, a Tier 1 agentic-eval fixture that exercises the by-reference source-storage path through the MCP store tool at the agent-observable (hook) surface. The fixture simulates an agent: 1. Calling store with source_storage='reference' and file_path — the hook records a tool_invocation entity whose input_summary captures the reference mode. 2. Calling retrieve_file_url for the available file — tool_output carries storage_mode='reference' with path metadata and no blob bytes. 3. Calling retrieve_file_url after the file is deleted — tool_output carries error='SOURCE_UNAVAILABLE' with the original path, not an exception. All five cursor-hooks × model cells pass (5/5). Includes pre-recorded snapshots for deterministic replay. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…e-source-storage # Conflicts: # docs/testing/automated_test_catalog.md
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🤖 Lanius — Ateles swarm, PR gate inheritance Parent issue #1775 has been triaged ( To proceed, the operator may confirm all pre-impl gates are clear via: This command waives all unsigned pre-impl gates (pm, ux, arch) on issue #1775 and enables review. 📎 Neotoma: issue #1775 |
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review:pm Pre-registered acceptance criteria verificationThis PR implements the feature scoped by issue #1775. Pavo pre-registered six acceptance criteria. The PM review checks whether the PR implementation satisfies each one. Criterion 1: Default
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review:ux User-facing surface & naming
Error & unavailability states
[NON-BLOCKING] Error message clarity — The DANGLING_REFERENCE message says «Eager derivation is required for reference sources — re-ingest with entities if needed.» This is correct but passive for an LLM. Suggest: «Reference source stored but no entities extracted. To materialize observations, re-ingest with entities or interpretations.» (more direct agency signal). Discoverability & documentation
[NON-BLOCKING] Docs gap — The schema doc is strong, but agents and developers new to reference mode will learn it from error messages + tests rather than from a guide. Suggest: add a one-page reference to the public docs (or inline to MCP_SPEC.md) covering the lifecycle and error states. Acceptance checklist
SummaryThe new surface is well-shaped for agent use. Parameter names are unambiguous, error codes are structured and distinct, and validation guides callers toward correct usage. The tool schema doc is thorough. One gap: a lightweight public-docs entry (1–2 paragraphs on when to use reference mode and what SOURCE_UNAVAILABLE means) would prevent agents from learning this surface only through trial-and-error. This is a non-blocking quality-of-life ask; the implementation is sound. |
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review:qa QA Review: By-Reference Source Storage (#1775)SummaryThis PR adds support for storing files by reference rather than copying bytes into blob storage. The change is evaluated against the agent-facing surface (MCP and endpoints) and test coverage for new edge cases. Coverage Assessment✅ Unit tests: Comprehensive coverage of reference resolution and hashing (9 tests, all passing).
✅ Integration tests: Direct MCP handler exercise (4 tests, all passing).
✅ Agentic eval: Fixture created and structured (cursor-hooks dist not built in CI, fixtures skipped but assertion shape is correct).
✅ Contract tests: All 146 passing (no new failures). Findings[NON-BLOCKING] Edge case: hash mismatch detection requires file access at retrieval time When a referenced file's content has drifted (hash stored in DB no longer matches actual file), detects this and returns . However:
Mitigation: Consider adding a companion observation (context_event or source_audit) when SOURCE_REFERENCE_STALE is returned, so operators can track reference drift. This is scope-manageable as a follow-up. [NON-BLOCKING] mismatch not tested The PR accepts from the stored reference metadata and includes it in the response. However, there is no test for the case where:
Impact: Mild. If a reference file path is absolute and accessible from host-B, retrieval succeeds regardless. The mismatch is informational but not enforced as a blocker. Suggested test: Store a reference on fake-host, then retrieve it from other-host and verify the response still works (path resolution is filesystem-based, not host-based). Confirmed Strengths
Regression Risk AssessmentLow. The PR extends the handler with an optional parameter (defaulting to inline) and adds a new path to for reference-mode lookups. Inline storage (existing behavior) is unaffected. Test Coverage Matrix
RecommendationApprove. Test coverage is adequate for the new agent-observable surfaces. Commit the agentic eval fixture so the turn-lifecycle assertions run in CI. The two non-blocking findings (drift detection observability and host_id mismatch testing) are scope-manageable follow-ups and do not block this PR. |
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review:content Verdict: APPROVE ✓This PR is shippable as a build-in-public content angle. It solves a real dogfooding constraint (large-file handling on resource-constrained hardware) and produces a clean, quotable design narrative. Content shippe-ability analysisThe story is strong: A non-developer evaluator hit a real problem — a 256GB Mac Mini couldn't absorb source bytes without bloating Neotoma's own DB. The feature is the direct response: "register a file without copying its bytes, but keep it first-class in the graph." That's a tight problem-solution fit, and the design shows discipline (content-addressed dedup still works; default The narrative hooks:
Test coverage supports the narrative: Full integration tests (reference storage, dedup on reference rows, resolveReferenceSource, dangling-reference warning shape). The snapshot-based agentic eval tests show the feature in the MCP tool interface — that's dogfooding proof. Positioned correctly for your audience: Builders running Neotoma locally on constrained hardware will clock this immediately. The implementation is honest (no "seamless" marketing language; just "local, depends on the file staying put"). No overstated promises. Downstream task (non-blocking)Filed a task in Corvus queue: "Draft build-in-public post on reference source storage." Shape will be:
This can ship alongside the PR or as a follow-up. No blocking dependency — the feature itself is solid and testable independent of external comms. No content blockers
Shippable. Ready to merge. |
…ndow (#1815) Headline features: by-reference source storage (#1775/#1803), disk-to-entity write-back via mirror push (#1776/#1802), Bundles m1-m4, sandbox showcase packs, cross-user read-leak hardening. Co-authored-by: ateles-agent <ateles-agent@markmhendrickson.com> Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
* docs(developer): add by-reference source storage + mirror write-back pages Public reference pages for the two v0.18.0 features (#1775/#1803, #1776/#1802) so they have real docs instead of only design issues. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * chore: regenerate capability manifest for the v0.18.0 tag The validate:capability-manifest gate walks release tags; after v0.18.0 was tagged, the committed manifest went stale on main (failing every branch). Regenerated. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: ateles-agent <ateles-agent@markmhendrickson.com> Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
3 participants
Summary
source_storage: 'inline' | 'reference'option to thestoreMCP tool (default'inline'— zero breaking changes). With'reference', the server reads the file once to compute SHA-256 + metadata and persists asourcesrow without storing the blob bytes.referencestore that produces zero observations emits aDANGLING_REFERENCEstore_warningsentry (warn-first, not a hard failure).retrieveFileUrlgains an optionalsource_idlookup that returnsSOURCE_UNAVAILABLEorSOURCE_REFERENCE_STALEstructured errors when the referenced file is missing or has drifted.Design
The authoritative architecture comment in #1775 guided the implementation:
content_hashis still computed at ingest (read-once-to-hash) and participates in theUNIQUE(content_hash, user_id)dedup index identically to inline sources.Source → Interpretation → Observationchain is unaffected. Reference sources link to interpretations and observations the same way inline sources do.sourcesviaaddColumnIfMissing(storage_modeTEXT NOT NULL DEFAULT 'inline',reference_path,host_id,size_bytes,mtime). All existing rows default tostorage_mode='inline'.Files changed
src/repositories/sqlite/sqlite_client.tsaddColumnIfMissingcalls for reference columnssrc/services/raw_storage.tsstoreRawReference,resolveReferenceSourceexports;SOURCE_UNAVAILABLE/SOURCE_REFERENCE_STALEstructured returnssrc/server.tssource_storageparam onstore(); reference branch; dangling-reference warning;retrieveFileUrlsource_idlookupsrc/tool_definitions.tssource_storageproperty onstoretool inputSchemasrc/services/__tests__/raw_storage_reference.test.tssrc/repositories/sqlite/__tests__/reference_storage.test.tsdocs/testing/automated_test_catalog.mdTest results
Closes #1775
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