jml 9bfa626203 docs: reorganize documentation structure for clarity

Major documentation restructure to improve discoverability and reduce duplication.

## Changes

**Deleted (Archived/Consolidated)**:
- Removed duplicate getting started guides
- Archived outdated planning documents
- Consolidated corpus and configuration docs
- Removed obsolete vision/spec files (superseded by vision.md)
- Cleaned up scrapyard and old PDFs

**New Structure**:
- docs/about/ - Project overview and introduction
- docs/guides/ - User guides (moved from root)
- docs/specs/ - Technical specifications
- docs/sdk/ - SDK documentation (Go)
- docs/references/ - API references
- docs/archive/ - Archived historical docs
- applications/aphoria/docs/advanced/ - Advanced topics
- applications/aphoria/docs/reference/ - CLI reference
- applications/aphoria/docs/archive/ - Archived aphoria docs

**Updated**:
- README.md - New root README with clear navigation
- CONTRIBUTING.md - Contribution guidelines
- CLAUDE.md - Updated paths to new structure
- roadmap.md - Added recent completions

## Files Changed
- 57 files changed
- 1,977 insertions(+)
- 961 deletions(-)

**Net change**: +1,016 lines (added CONTRIBUTING.md, README.md, reorganized content)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

2026-02-11 07:33:40 +00:00

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Corpus Quick Start Guide

TL;DR - API is Already Running!

The corpus API is currently serving data at:

URL: http://localhost:18180/v1/aphoria/corpus
Database: ~/.aphoria/corpus-db
Data: 2 RFC items (TLS cert verification, JWT audience validation)

Test It Right Now

# Get all RFC corpus items
curl -s 'http://localhost:18180/v1/aphoria/corpus?sources[]=rfc' | jq '.items[].subject'

# Expected output:
# "rfc://5246/tls/certificate_verification"
# "rfc://7519/audience_validation"

Import Production Wiki

cd ~/Workspace/stemedb
target/release/aphoria corpus import wiki ~/Workspace/orchard9/wiki/content

Start Dashboard

cd applications/aphoria-dashboard
npm run dev
# Open: http://localhost:3000/corpus

Restart API Later (if needed)

cd ~/Workspace/stemedb
STEMEDB_DB_DIR=$HOME/.aphoria/corpus-db \
STEMEDB_WAL_DIR=$HOME/.aphoria/corpus-db/wal \
target/release/stemedb-api

Query Examples

# Get all sources (RFC, OWASP, vendor, community)
curl 'http://localhost:18180/v1/aphoria/corpus'

# Filter by multiple sources
curl 'http://localhost:18180/v1/aphoria/corpus?sources[]=rfc&sources[]=owasp'

# Filter by category
curl 'http://localhost:18180/v1/aphoria/corpus?category=security'

# Pagination
curl 'http://localhost:18180/v1/aphoria/corpus?limit=10&offset=0'

Response Format

{
  "items": [
    {
      "subject": "rfc://5246/tls/certificate_verification",
      "predicate": "enabled",
      "value": "true",
      "source": "rfc://",
      "tier": 0,
      "category": "security",
      "explanation": "TLS certificate verification MUST be enabled...",
      "authority_source": "RFC 5246 Section 7.4.2"
    }
  ],
  "total_matching": 2,
  "sources_included": ["rfc://"]
}

Files to Know

Corpus DB: ~/.aphoria/corpus-db/ (shared across projects)
Project DB: .aphoria/db/ (per-project)
Import CLI: aphoria corpus import wiki <path>
API Config: Set STEMEDB_DB_DIR to choose database

Troubleshooting

Dashboard shows empty results?

Check API is running on port 18180
Verify API is using corpus database: ps aux | grep stemedb-api
Check API logs for database path

API won't start?

Make sure corpus DB exists: ls ~/.aphoria/corpus-db/
Check port not in use: lsof -i :18180
View logs: tail -f /tmp/api-corpus.log

Need to reimport wiki?

rm -rf ~/.aphoria/corpus-db
target/release/aphoria corpus import wiki <path>

✅ Current Status: API running, corpus database populated, ready for dashboard!

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