Fixed 3 bugs in Aphoria's claim verification engine that were causing
false positives in Maxwell validation testing:
**Bug 1: Path matching + predicate filtering**
- Added predicate filtering to prevent cross-predicate matches
- Added path prefix matching to respect crate boundaries
- Prevents core/imports/serde from matching hypervisor/vsock/imports/serde
**Bug 2: Value-specific absent checks**
- Absent mode now checks for specific forbidden value, not any observation
- Example: "Clone absent" + "Debug present" = PASS (not CONFLICT)
- Only conflicts when the exact forbidden value is found
**Bug 3: Wildcard pattern support**
- Wildcard patterns like message/*/derives now match multiple paths
- Enhanced wildcard_matches() to support prefix/*/suffix patterns
- Correctly strips full scheme+language from observation paths
**Test coverage:**
- All 39 existing tests passing
- 3 new tests added for bug fixes
- 2 tests updated to use correct predicates
- Zero clippy warnings
**Maxwell validation:**
- maxwell-core-no-serde-001: CONFLICT → PASS (respects path boundaries)
- maxwell-singleton-no-clone-001: CONFLICT → PASS (value-specific absent)
- 5 claims now correctly show as MISSING (expose predicate mismatches)
The fixes successfully eliminate false positives while exposing pre-existing
issues where claims used incorrect predicates.
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>
- Add benchmark: false to ScanArgs in stemedb-api handler
- Change test float from 3.14 to 7.25 to avoid clippy approx_constant
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>
- 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>
Content Defense (Phase 7):
- Add SimilarityIndex with MinHash/LSH for near-duplicate detection
- Add QuarantineStore for flagged assertions awaiting admin review
- Add CircuitBreakerStore for per-agent circuit breaker state
- Add ContentDefenseLayer for ingestion pipeline integration
- Add API endpoints for quarantine and circuit breaker management
- Add research module with gap detection and documentation fetching
Code Structure Improvements:
- Extract research CLI commands to research_commands.rs
- Extract API routers to routers.rs module
- Extract key_codec extraction functions to separate module
- Extract test modules to separate files across multiple crates
- All files now under 500 line limit per pre-commit hook
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add Hybrid Logical Clock (HLC) for causality tracking across nodes
- Implement Merkle tree for efficient diff/sync with BLAKE3 hashing
- Add CRDT-aware stores for assertions and votes with vector clocks
- Create stemedb-sync crate with anti-entropy and gossip protocols
- Add stemedb-rpc crate with gRPC sync service (proto definitions)
- Implement SupersessionChain for tracking assertion lifecycles
- Add Aphoria application for code analysis/reporting
- Add battery11 replication test scaffolding
- Fix .gitignore to exclude nested target directories
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add CRC32C checksums to WAL record format (v2), implement crash recovery
with automatic truncation of corrupt records, add feature-gated group commit
buffer for batched fsync under concurrent load, and implement log rotation
via segment files with global offset addressing.
Key changes:
- Record format v2: [len:u32][crc32c:u32][blake3:32][payload:N]
- recover_file() scans and truncates corrupt tail records
- GroupCommitBuffer batches fsync via MPSC channel (tokio feature gate)
- SegmentManager with binary search resolution and cursor-based cleanup
- Journal::read() auto-refreshes segments on miss for writer/reader split
- Split recovery.rs and key_codec.rs into directory modules for 500-line max
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>
