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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
.agentive-remediation feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
.cargo Initial project setup with Claude Code monorepo structure 2026-01-31 10:56:26 -07:00
.claude feat: add Aphoria dashboard scans and corpus UI 2026-02-07 15:56:49 -07:00
ai-lookup feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
applications feat(aphoria): implement ignore & exclusion system (Phase 16) 2026-02-07 17:28:50 -07:00
batteries feat: WAL hardening (Phase 5B) - CRC32C, crash recovery, group commit, log rotation 2026-02-02 12:36:35 -07:00
cmd feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
community feat: Ingestor deadlock fix + blessed assertion tracking + patent docs 2026-02-04 03:41:08 -07:00
crates feat: add Aphoria dashboard scans and corpus UI 2026-02-07 15:56:49 -07:00
demo/keys feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
docs feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
latent feat: Multi-application expansion with chaos testing and community UI 2026-02-04 01:24:14 -07:00
scripts feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
sdk/go feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
uat feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
use-cases feat: Multi-application expansion with chaos testing and community UI 2026-02-04 01:24:14 -07:00
.aphoriaignore feat(aphoria): implement ignore & exclusion system (Phase 16) 2026-02-07 17:28:50 -07:00
.dockerignore feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
.gitignore feat: add Aphoria dashboard scans and corpus UI 2026-02-07 15:56:49 -07:00
.jscpd.json Initial project setup with Claude Code monorepo structure 2026-01-31 10:56:26 -07:00
aphoria.toml feat(aphoria): implement ignore & exclusion system (Phase 16) 2026-02-07 17:28:50 -07:00
architecture.md feat: Complete Phase 2 (The Cortex) - query, lens, and API layers 2026-02-01 13:22:44 -07:00
arena-roadmap.md refactor: Split all files to enforce 500-line max 2026-02-02 01:13:45 -07:00
Cargo.toml feat: Aphoria scan modes + stemedb-ontology crate + consumer health UAT 2026-02-04 21:57:33 -07:00
CLAUDE.md feat: add aphoria-install skill for user-space installation 2026-02-07 07:47:54 -07:00
clippy.toml Initial project setup with Claude Code monorepo structure 2026-01-31 10:56:26 -07:00
CODING_GUIDELINES.md Initial project setup with Claude Code monorepo structure 2026-01-31 10:56:26 -07:00
docker-compose.yml feat: Multi-application expansion with chaos testing and community UI 2026-02-04 01:24:14 -07:00
Dockerfile feat: Multi-application expansion with chaos testing and community UI 2026-02-04 01:24:14 -07:00
GEMINI.md feat: Complete Phase 1 (The Spine) - storage foundation 2026-01-31 14:15:34 -07:00
Makefile feat: Add quickstart "Beyond Hello World" sections with Skeptic and Layered endpoints 2026-02-01 21:00:59 -07:00
position.md feat: Complete Phase 2 (The Cortex) - query, lens, and API layers 2026-02-01 13:22:44 -07:00
quickstart.md feat: Multi-application expansion with chaos testing and community UI 2026-02-04 01:24:14 -07:00
roadmap-archive.md feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
roadmap.md feat: Complete Aphoria Phase 8-9 + UAT suite (90/90 tests passing) 2026-02-06 22:50:55 -07:00
rustfmt.toml Initial project setup with Claude Code monorepo structure 2026-01-31 10:56:26 -07:00
simulation-vision.md feat: Complete Phase 1 (The Spine) - storage foundation 2026-01-31 14:15:34 -07:00
stemedb.pdf feat: Multi-application expansion with chaos testing and community UI 2026-02-04 01:24:14 -07:00
usage.md feat: Multi-application expansion with chaos testing and community UI 2026-02-04 01:24:14 -07:00
vision.md feat: Complete Aphoria Phase 14 - Governance Workflows 2026-02-07 05:16:26 -07:00
what-is-episteme.md feat: WAL hardening (Phase 5B) - CRC32C, crash recovery, group commit, log rotation 2026-02-02 12:36:35 -07:00