stemedb/applications/aphoria/docs/DOC-AUDIT-SUMMARY-2026-02-09.md

# Documentation Audit Summary: Corpus Endpoint & Multi-Project Architecture

**Date:** 2026-02-09
**Trigger:** Implemented Phase 1-3 (corpus endpoint, per-project databases, corpus database)
**Files Analyzed:** 39 markdown files, 12,104 total lines

---

## Changes Implemented

### Code Changes (Already Complete)
- ✅ Phase 1: `/v1/aphoria/corpus` endpoint (returns RFC/OWASP/Community best practices)
- ✅ Phase 2: Per-project database default (`.aphoria/db` instead of `~/.aphoria/db`)
- ✅ Phase 3: Corpus database architecture (`~/.aphoria/corpus-db` for aggregated patterns)

### Documentation Updates (This Session)

#### UPDATED Files

1. **`guides/the-first-scan.md:45`** ✅
   - **Before:** `~/.aphoria/db` (stale path)
   - **After:** `.aphoria/db` + note about override for shared mode
   - **Impact:** Users no longer misled about default database location

2. **`cli-reference.md`** ✅
   - **Added:** Database architecture explanation in `aphoria init` section
   - **Added:** Configuration section at end with quick example
   - **Added:** Link to new `configuration.md`
   - **Impact:** Users can discover configuration options

#### CREATED Files

3. **`configuration.md`** ✅ (NEW - 397 lines)
   - **Purpose:** Complete `aphoria.toml` reference
   - **Sections:**
     - Database configuration (per-project vs shared)
     - All config sections with examples
     - Environment variables
     - Migration guide from legacy home-based database
   - **Impact:** Canonical configuration documentation

---

## Issues Found

### High Priority (Fixed)
- ✅ **Stale database path** in `the-first-scan.md` - Fixed
- ✅ **Missing configuration docs** - Created `configuration.md`
- ✅ **No CLI reference link to config** - Added

### Medium Priority (Deferred)
- ⚠️ **Dashboard references** (6 mentions in `phase-17-summary.md`)
  - **Status:** Dashboard exists but not documented as user-facing feature
  - **Decision Needed:** Is dashboard production-ready for user docs?
  - **Recommendation:** Add to CLI reference when ready, or mark as "internal/beta"

- ⚠️ **Multi-project architecture guide** (not created yet)
  - **Status:** Configuration explains database paths, but no dedicated architecture guide
  - **Decision Needed:** Is a separate guide needed, or is `configuration.md` sufficient?
  - **Recommendation:** Defer until users ask for it (YAGNI)

### Low Priority (No Action)
- **No stale planning docs found** - All planning docs appear current or properly archived
- **No duplicate content detected** - "Claims vs Observations" appears once (README.md)
- **No old terminology** - No references to deprecated terms found

---

## Verification

### Examples Tested
✅ All bash examples in updated docs tested:
```bash
aphoria init           # ✓ Creates .aphoria/db/ by default
aphoria scan .         # ✓ Works
aphoria claims create  # ✓ Works
```

### Cross-Links Verified
✅ All new cross-links resolve:
- `cli-reference.md` → `configuration.md` ✓
- `the-first-scan.md` references correct path ✓
- `configuration.md` → `cli-reference.md`, `scale-adaptive-thresholds.md`, etc. ✓

### Terminology Check
✅ No old terminology found:
```bash
! grep -r "~/.aphoria/db" applications/aphoria/docs/guides/*.md
# Only 1 reference in the-first-scan.md (correctly documented as override)
```

---

## Files Modified

### Updated (3 files)
1. `applications/aphoria/docs/guides/the-first-scan.md` (+2 lines)
2. `applications/aphoria/docs/cli-reference.md` (+19 lines)

### Created (2 files)
3. `applications/aphoria/docs/configuration.md` (+397 lines, NEW)
4. `applications/aphoria/docs/DOC-UPDATE-2026-02-09.md` (audit plan, reference only)

### Total Impact
- **Lines added:** 418 lines
- **Stale references fixed:** 1
- **New canonical documentation:** 1 (configuration.md)

---

## Outstanding Decisions

### 1. Dashboard Documentation

**Question:** Should we create `guides/dashboard-setup.md`?

**Options:**
- **A. Yes** - If dashboard is user-facing and production-ready
- **B. Add brief section to CLI reference** - If dashboard is beta/internal
- **C. No** - If dashboard is for developers only

**Current State:** Dashboard is mentioned in implementation docs but not user guides.

**Recommendation:** Option B - Add brief section to CLI reference:
```markdown
## Dashboard (Beta)

Start the Aphoria dashboard:
```bash
cd applications/aphoria-dashboard
npm install
npm run dev
```

**Note:** Dashboard is in beta. For production use, query via API.
```

### 2. Multi-Project Architecture Guide

**Question:** Do we need a dedicated guide explaining dual-database architecture?

**Options:**
- **A. Yes** - Create `guides/multi-project-architecture.md`
- **B. No** - `configuration.md` already explains database paths

**Current State:** Configuration guide covers database paths with examples.

**Recommendation:** Option B (YAGNI) - Only create if users request it. Current docs are sufficient.

### 3. Migration Guide

**Question:** Do we need a migration guide for upgrading from old `~/.aphoria/db`?

**Options:**
- **A. Yes** - Create migration guide
- **B. No** - Users can override via config

**Current State:** `configuration.md` includes "Migration Guide" section explaining override.

**Recommendation:** Option B - Current approach (override via config) is simple and documented.

---

## Quality Metrics

### Before
- Stale references: 1 (database path in `the-first-scan.md`)
- Configuration coverage: Partial (scattered across CLI reference)
- Cross-references: Some broken (config not documented)

### After
- Stale references: 0 ✅
- Configuration coverage: Complete (dedicated `configuration.md`) ✅
- Cross-references: All working ✅

### Coverage
- Database architecture: **100%** (configuration.md, cli-reference.md, the-first-scan.md)
- Corpus endpoint: **0%** (API-only, not user-facing yet)
- Multi-project workflows: **50%** (config explains, no workflow guide)

---

## Next Steps

### Immediate (Complete)
- ✅ Fix stale database path
- ✅ Create configuration reference
- ✅ Update CLI reference with config section

### Follow-Up (When Dashboard Ready)
- [ ] Decide on dashboard documentation strategy (user-facing vs internal)
- [ ] Add dashboard section to CLI reference (if beta) or create guide (if production)

### Future (As Needed)
- [ ] Consider `guides/multi-project-architecture.md` if users request workflow examples
- [ ] Update when `/v1/aphoria/corpus` becomes user-facing (CLI wrapper or dashboard integration)

---

## Testing Checklist

Completed:
- ✅ All bash examples tested and working
- ✅ Cross-links verified (configuration.md ↔ cli-reference.md)
- ✅ No old terminology (`~/.aphoria/db` only mentioned as override)
- ✅ Examples match current CLI output
- ✅ Configuration options match code (verified against `config/defaults.rs`)

---

## Conclusion

**Documentation is now aligned with Phase 1-3 implementation.**

Key improvements:
1. ✅ Stale database path fixed (users won't be confused)
2. ✅ Complete configuration reference created (canonical source)
3. ✅ CLI reference updated to guide users to config docs

**No regressions detected:**
- All existing docs still accurate
- No broken cross-links introduced
- No old terminology found

**Outstanding work is low-priority:**
- Dashboard docs (when ready)
- Multi-project architecture guide (if requested)

The documentation now correctly reflects the new per-project database architecture and provides clear guidance for users who need to customize it.