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65065f3d8f
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Author SHA1 Message Date
jml
65065f3d8f feat(aphoria): implement community corpus with wiki import and pattern aggregation 
Implements Phase 4 (A4) - Community corpus as first-class citizens:

- **Community Corpus Builder** - Queries StemeDB pattern aggregates
- **Wiki Import** - Bootstrap corpus from markdown docs (aphoria corpus import wiki)
- **Pattern Aggregation** - Automatic learning from local scans (--sync flag)
- **Storage Layer** - StemeDBPatternStore with content-addressed deduplication
- **Promotion Logic** - Multi-tier thresholds (95%/80%/50% adoption rates)
- **Corpus Build** - Unified registry for RFC/OWASP/Vendor/Community sources
- **Trust Packs** - Export corpus as signed, distributable artifacts
- **Documentation** - bootstrap-corpus.md guide + CLI reference updates

Technical details:
- Pattern aggregates stored as assertions with predicate "pattern_aggregate"
- Content-addressed subjects via BLAKE3(subject:predicate:value)
- PatternAggregator handles write path (observations → patterns)
- StemeDBPatternStore handles read path (pattern queries)
- Integration tests + fixtures in tests/wiki_import_test.rs

Deleted hardcoded.rs (368 lines) - corpus now fully emergent from StemeDB.
Deleted enriched-corpus-patterns.md (677 lines) - feature shipped.

Closes VG-026 (community corpus), part of A4 milestone.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
 2026-02-09 00:12:31 +00:00
jml
6430ff0fd6 fix(aphoria): move claims.toml to project root and fix verify integration 
## Root Cause
Claims file was in applications/aphoria/.aphoria/ but all commands looked
for .aphoria/claims.toml relative to project root. Additionally, .aphoria/
was fully gitignored, preventing version control of claims.

## Changes

### Path Fixes
- Move claims.toml from applications/aphoria/.aphoria/ to .aphoria/ at project root
- Update .gitignore: .aphoria/ → .aphoria/* with !.aphoria/claims.toml exception
- Now claims can be version controlled while keys remain secret

### Verify Integration (Scanner)
- scanner.rs: Load claims from ClaimsFile and call verify_claims()
- ScanResult: Add verify field with VerifyReport
- Report formatters: Add claim verification sections showing PASS/CONFLICT/MISSING

### Clippy Fix
- report/json.rs: Replace filter().map().expect() with filter_map()

## Verification
- aphoria scan . → Shows claim verification with verdicts
- aphoria verify run → Per-claim verification results
- aphoria verify map → Extractor coverage mapping (7/10 claims = 70%)
- aphoria claims list → Reads from project root
- aphoria claims create → Writes to project root
- All tests pass (1120+ aphoria tests)
- clippy --workspace passes

## Impact
Both primary use cases now work:
1. Day-to-day (commit-time): Skills can read/create claims via CLI
2. Audit (scan-time): Scanner verifies code against authored claims

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
 2026-02-08 11:09:57 +00:00
jml
3b5f88b4f0 feat(aphoria): implement claims architecture (A1-A5) with verify engine, corpus, coverage, and explain 
Complete Aphoria claims system overhaul:
- A1: Rename ExtractedClaim to Observation (extractors produce observations, not claims)
- A2: Add AuthoredClaim with full provenance, invariants, and authority tiers
- A3: Verify engine comparing observations against authored claims, CLI + formatters
- A4: Corpus as first-class assertions with predicate indexing, authority lens, trust packs
- A5: Coverage analysis, explain/docs generation, self-audit extractor, claim suggester skill

Also includes: 42 extractors updated for Observation type, verifiable_predicates trait,
conflict detection with comparison modes, claims TOML persistence, Grafana dashboard,
backup/restore scripts, and comprehensive test coverage.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-02-08 09:11:47 +00:00
jml
e73bf3c4b7 feat(aphoria): add --show-claims flag to display all extracted claims 
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>
 2026-02-08 00:39:54 +00:00
jordan
c65066fd1c feat(aphoria): implement ignore & exclusion system (Phase 16) 
Reduces scan noise by 96% through proper exclusion of test fixtures,
demo apps, and intentional vulnerabilities.

Phase 16.1 - Glob Pattern Matching:
- Replace starts_with() with globset for ** and * patterns
- Backwards compatible with legacy prefix patterns
- Add walker/mod.rs tests for glob exclusions

Phase 16.2 - .aphoriaignore File:
- Create walker/ignore_file.rs for gitignore-style parsing
- Merge with aphoria.toml excludes
- Support # comments and whitespace trimming

Phase 16.3 - Inline Ignore Comments:
- Create extractors/ignore_comments.rs parser
- Support // aphoria:ignore, // aphoria:ignore-next-line
- Support // aphoria:ignore-block / // aphoria:end-ignore
- Multiple comment styles: //, #, /*, --, <!--
- Integrate with ExtractorRegistry.extract_all()

Phase 16.4 - Ack Export/Import:
- Create ack_file.rs for TOML serialization
- Add 'aphoria ack add' subcommand
- Add 'aphoria ack export' to .aphoria/acks.toml
- Add 'aphoria ack import' from .aphoria/acks.toml
- Preserve expiry and reason fields

Also configures stemedb with:
- aphoria.toml with glob excludes for vulnbank, extractors, fixtures
- .aphoriaignore for dashboard, community, latent, SDK examples

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2026-02-07 17:28:50 -07:00
jordan
c849627620 feat: add Aphoria dashboard scans and corpus UI 
- 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>
 2026-02-07 15:56:49 -07:00
jordan
8af9b48ac7 feat: Complete Aphoria Phase 14 - Governance Workflows 
Implement structured approval workflows for pattern promotion with full
audit trails for SOC 2 compliance.

Core Components:
- governance/types.rs: ApprovalRequest, ApprovalStatus, ApprovalDecision
- governance/workflow.rs: ApprovalWorkflow, ApprovalStage with escalation
- governance/store.rs: JSONL persistence for requests and decisions
- governance/state_machine.rs: Approval state transitions with auto-advance
- governance/audit.rs: AuditTrail with JSON/CSV/Markdown export

CLI Commands:
- aphoria governance pending/approve/reject/escalate/status/create
- aphoria audit trail/export/summary

Integration:
- Pipeline gate blocks promotion until governance approval
- Auto-creates approval requests when governance enabled
- Evidence-based auto-approval for high-confidence patterns

Also includes:
- Phase 11-13: Evidence, Lifecycle, Scope modules
- 62+ governance-specific tests (946 total passing)
- Clippy clean with -D warnings
- Refactored cli.rs into submodules (governance, lifecycle, scope, etc.)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2026-02-07 05:16:26 -07:00