## Problem
CLI-created community corpus items (tier 3) were stored correctly but
invisible via API queries. Two issues blocked discoverability:
1. **Prefix mismatch**: API hardcoded 'community://pattern/' for
aggregated patterns, but CLI creates 'community://rust/http/...' URIs
2. **Query parameter parsing**: Axum's default parser doesn't support
bracket notation (?sources[]=value) used by the dashboard
Result: 0/22 CLI-created items were queryable.
## Solution
### Fix 1: Broaden Community Prefix
- Changed: 'community://pattern/' → 'community://' in corpus handler
- Impact: Now matches both aggregated patterns AND CLI-created items
- Backward compatible: Broader prefix includes narrower results
### Fix 2: Add QsQuery Extractor
- Added: serde_qs dependency + custom QsQuery extractor
- Supports: Bracket notation for array parameters (?sources[]=a&sources[]=b)
- Compatible: Works with JavaScript URLSearchParams standard
- Tested: 3 new unit tests for extractor behavior
## Verification
- ✅ All 22 CLI-created community items now queryable (was 0)
- ✅ Source filtering works: community (22), RFC (2), vendor (5)
- ✅ Multi-source queries work: ?sources[]=community&sources[]=rfc → 24
- ✅ All 89 API tests pass + 3 new extractor tests
- ✅ Clippy clean (0 warnings)
- ✅ No regressions in existing functionality
## Files Changed
- crates/stemedb-api/Cargo.toml: Add serde_qs dependency
- crates/stemedb-api/src/extractors.rs: New QsQuery extractor (117 lines)
- crates/stemedb-api/src/handlers/aphoria/corpus.rs: Use QsQuery, broaden prefix
- crates/stemedb-api/src/lib.rs: Export extractors module
Also includes: Scale-adaptive thresholds, wiki corpus extraction,
documentation updates, and dashboard UI improvements from prior work.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
This commit implements Phase 17 of the Aphoria roadmap, adding:
**Inline Claim Markers (@aphoria:claim):**
- New extractor for detecting inline markers in comments
- Pending markers tracked in .aphoria/pending_markers.toml
- CLI commands: list-markers, formalize-marker, reject-marker
- Support for all major comment styles (Rust, Python, SQL, etc.)
- Auto-sync during scan (configurable)
**Claim Enrichment:**
- ClaimEnrichment type with source attribution (inline, extractor, manual)
- EnrichedClaimInfo with full enrichment metadata
- Extended AuthoredClaim with optional enrichment field
- API endpoints for enriched claim queries
- Dashboard UI components (enrichment badge, verdict badge)
**Enhanced Extractor Trait:**
- verifiable_predicates() method for declaring (tail_path, predicate) pairs
- 10 security extractors now implement verifiable_predicates
- Enables claim suggester skill to find unclaimed patterns
**Documentation:**
- Phase 17 summary with complete implementation details
- Gap fixes summary documenting 8 closed vision gaps
- Updated CLI reference with new commands
- New aphoria-docs skill for documentation maintenance
- Updated roadmap with Phase 17 completion
**Integration:**
- ClaimsFile support for claim enrichment persistence
- Pattern aggregate store support for enrichment queries
- Dashboard filters and display for enrichment metadata
- API handlers for list-markers and enrichment queries
**Tests:**
- New gap_fixes_integration test suite
- Corpus enricher module with best practices ingestion
Closes: VG-005, VG-017, VG-018, VG-019, VG-020, VG-021, VG-022, VG-023
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Add scans panel with finding details, verdict badges, and filters
- Add corpus panel for managing knowledge sources
- Add scan cache for API state management
- Update sidebar navigation with new routes
- Extend API types for scans and corpus endpoints
- Add .aphoria/ to gitignore (contains project keys)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When installation encounters bugs or unexpected behavior, the skill now:
- Creates notes in ~/.aphoria/notes/{date}-{issue}.md
- Documents environment, steps to reproduce, errors, workarounds
- Checks for existing notes before starting new installs
- Includes note format template with tags for categorization
This creates a feedback loop for improving installation experience
based on real-world issues.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Creates skill for installing and running StemeDB/Aphoria:
- Three installation tiers: Solo, Team, Enterprise
- Step-by-step installation protocol (prerequisites, build, init, verify)
- Optional StemeDB server setup for team observation aggregation
- Troubleshooting section for common issues
- Uninstall instructions
- Environment variable reference
Routing added to CLAUDE.md for discoverability.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Enterprise Features:
- Hosted mode with remote sync for team pattern aggregation
- Community sharing with privacy-preserving anonymization
- LLM-based semantic claim extraction with Gemini integration
- Pattern learning with promotion to declarative extractors
- High-entropy secrets extractor with configurable thresholds
- Auth bypass and insecure cookies extractors
Module Refactoring:
- Split oversized files to comply with 500-line limit
- Config split: types/core.rs, types/extractors.rs, types/hosted.rs, etc.
- Handlers split: scan.rs, policy.rs, report.rs modules
- Extractors split: declarative/, high_entropy_secrets/, insecure_cookies/
- Learning split: store modules with metrics and persistence
SDK & Ontology:
- stemedb-ontology SDK with fluent builders and StemeDB client
- Pharma domain extractors for FDA Orange Book data
- Consumer health UAT test infrastructure
Code Quality:
- Fixed clippy warnings (needless_borrows_for_generic_args)
- Added KVStore trait imports where needed
- Fixed utoipa path re-exports for OpenAPI docs
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Major additions:
- Staged scanning modes (working tree, staged, committed) with git integration
- Drift detection for baseline vs current state comparisons
- Hosted API handlers for policy CRUD operations via StemeDB API
- stemedb-ontology crate with domain definitions and medical extractors
- Consumer health vertical UAT scenarios (GLP-1, gastroparesis, etc.)
- Aphoria development skill documentation
Code organization:
- Split large files into focused modules to stay under 500-line limit
- Extracted config tests, episteme helpers/drift/aliases, API helpers
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Key changes:
- Fix Ingestor background task to release lock per iteration, preventing
deadlock when process_pending() needs the lock during shutdown
- Add blessed assertion predicate index and fetch_blessed_assertions()
for policy export workflows in Aphoria
- Add patent documentation (markdown + Word exports) for probabilistic
knowledge graph system
- Update community scripts for claim extraction pipeline
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add PolicySourceStore for tracking where policies come from
- Implement claim extraction skill and API endpoints
- Add community UI text selection extractor component
- Create Go SDK aphoria client for policy operations
- Document patent specifications and legal disclosures
- Add guides: golden path loop, policy audit trails, pre-flight checks
- Expand Unreal Engine config extractor with source tracking
- Add UAT reports for policy source tracking validation
- Refactor tests.rs into modular test files
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add Layered() method to Go SDK for per-source-class consensus queries
- Add LayeredQueryParams, LayeredResult, TierResolution types to Go SDK
- Create conflict example demonstrating Skeptic and Layered endpoints
- Update quickstart.md with sections 6 (conflict detection) and 7 (authority tiers)
- Remove tracked Go binary and add data/ to .gitignore
The new quickstart sections demonstrate Episteme's differentiating features:
- Skeptic endpoint shows "Trust but Verify" conflict analysis
- Layered endpoint shows per-tier resolution (Clinical vs Anecdotal)
Note: Pre-existing large files flagged by pre-commit hook (technical debt from prior sessions)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 1 delivers the complete durability and storage layer:
- WAL with crash recovery: Append-only journal with BLAKE3 checksums,
fsync guarantees, and proper seek-to-EOF on reopen
- Storage engine: sled-backed KVStore with scan_prefix for range queries
- Content-addressed storage: H:{hash}, V:{hash}, E:{hash} key patterns
- Ingestor: Background worker tailing WAL, writing to KV with 8-byte
aligned record headers for rkyv zero-copy deserialization
- Comprehensive tests: 31 tests covering crash recovery, round-trips,
and multi-cycle durability
New crates: stemedb-wal, stemedb-storage, stemedb-ingest
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
