Implements the --show-claims feature requested by users who need to verify
extractors are working correctly and debug false negatives.
Changes:
- Add `claims: Option<Vec<ExtractedClaim>>` field to ScanResult
- Add `--show-claims` CLI flag to scan command
- Add `show_claims: bool` parameter to ScanArgs
- Populate claims in scanner when flag is set (sorted by file, then line)
- Display claims in all output formats:
* Table: New "Extracted Claims" section with concept/value/file/line/confidence
* JSON: Top-level `claims` array with full claim details
* Markdown: "## Extracted Claims" section with table
* SARIF: Informational-level results (level: "note") for IDE integration
User outcome:
- `aphoria scan . --show-claims` displays all claims (not just conflicts)
- Users can verify extractors detected their code patterns
- Users can debug false negatives by seeing what WAS extracted
- Builds trust through transparency
Quality:
- Zero breaking changes (opt-in flag, backward compatible)
- All tests passing (943 passed)
- Clippy clean (no warnings)
- Manual testing verified all 4 output formats
Addresses user feedback from /home/jml/Workspace/maxwell/.aphoria/.notes-for-aphoria-team
Co-Authored-By: Claude Opus 4.6 <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>
- Created solo-developer-guide.md for individual/side projects
- Created enterprise-pilot-guide.md with 7-phase pilot methodology
- Updated guides/README.md with new guide references
- Updated main README.md with guides table and time estimates
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>
Use `super::*` instead of `super::tls_version::TlsVersionExtractor` since
the test module is included via #[path] inside tls_version.rs.
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>
- Use std::slice::from_ref instead of &[x.clone()]
- Avoid approx_constant lint with explicit f64 suffix
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>
