docs: update GAP_ANALYSIS.md for current state

- Remove silo-spec.md from doc table (deleted)
- Add CONFIGURATION.md, AUTH.md, AUTH_USER_GUIDE.md, frontend-spec.md to doc table
- Mark Configuration Reference as complete
- Fix audit_handlers.go filename (was handlers_audit.go)
- Update Appendix A file structure to match actual codebase
- Fix future migration numbering (012/013, since 011 is taken)
- Add file attachment endpoints to Appendix B
- Remove completed Documentation Overhaul from medium-term

Closes #28

docs/GAP_ANALYSIS.md

@@ -1,6 +1,6 @@
 # Silo Gap Analysis and Revision Control Roadmap
 
-**Date:** 2026-02-06  
+**Date:** 2026-02-08  
 **Status:** Analysis Complete (Updated)
 
 ---
@@ -21,9 +21,12 @@ This document analyzes the current state of the Silo project against its specifi
 | `docs/SPECIFICATION.md` | Design specification, API reference | Current |
 | `docs/STATUS.md` | Implementation status summary | Current |
 | `docs/DEPLOYMENT.md` | Production deployment guide | Current |
-| `docs/GAP_ANALYSIS.md` | SOLIDWORKS PDM comparison, roadmap | Current |
-| `ROADMAP.md` | Feature roadmap and phases | Current |
-| `silo-spec.md` | Redirect to `docs/SPECIFICATION.md` | Consolidated |
+| `docs/CONFIGURATION.md` | Configuration reference (all config.yaml options) | Current |
+| `docs/AUTH.md` | Authentication system design | Current |
+| `docs/AUTH_USER_GUIDE.md` | User guide for login, tokens, and roles | Current |
+| `docs/GAP_ANALYSIS.md` | Revision control roadmap | Current |
+| `ROADMAP.md` | Feature roadmap and SOLIDWORKS PDM comparison | Current |
+| `frontend-spec.md` | React SPA frontend specification | Current |
 
 ### 1.2 Documentation Gaps (Priority Order)
 
@@ -34,7 +37,7 @@ This document analyzes the current state of the Silo project against its specifi
 | **API Reference** | Users cannot integrate programmatically | Medium | Addressed in SPECIFICATION.md Section 11 |
 | **Deployment Guide** | Cannot deploy to production | Medium | Complete (`docs/DEPLOYMENT.md`) |
 | **Database Schema Guide** | Migration troubleshooting difficult | Low | Open |
-| **Configuration Reference** | config.yaml options undocumented | Low | Open |
+| **Configuration Reference** | config.yaml options undocumented | Low | Complete (`docs/CONFIGURATION.md`) |
 
 #### Medium Priority
 
@@ -54,10 +57,10 @@ This document analyzes the current state of the Silo project against its specifi
 
 ### 1.3 Recommended Actions
 
-1. ~~**Consolidate specs**: Remove `silo-spec.md` duplicate~~ Done
+1. ~~**Consolidate specs**: Remove `silo-spec.md` duplicate~~ Done (deleted)
 2. ~~**Create API reference**: Full REST endpoint documentation~~ Addressed in SPECIFICATION.md
 3. ~~**Create `docs/DEPLOYMENT.md`**: Production deployment guide~~ Done
-4. **Create configuration reference**: Document all `config.yaml` options
+4. ~~**Create configuration reference**: Document all `config.yaml` options~~ Done (`docs/CONFIGURATION.md`)
 5. **Create database schema guide**: Document migrations and troubleshooting
 
 ---
@@ -207,7 +210,7 @@ Audit logging is implemented via migration 009 with the `audit_log` table and co
 - `GET /api/audit/completeness` — summary of all items
 - `GET /api/audit/completeness/{partNumber}` — per-item scoring with weighted fields and tier classification
 
-Code: `internal/api/handlers_audit.go`
+Code: `internal/api/audit_handlers.go`
 
 ---
 
@@ -304,7 +307,6 @@ Effort: Medium | Priority: Low | Risk: Low
 
 7. **Release Management** - Product milestone tracking
 8. **Thumbnail Generation** - Visual preview capability
-9. **Documentation Overhaul** - API reference, deployment guide
 
 ### Long-term (Future)
 
@@ -351,19 +353,33 @@ These design decisions remain unresolved:
 
 ## Appendix A: File Structure
 
-Revision endpoints, status, labels, authentication, and audit logging are implemented. Current structure:
+Revision endpoints, status, labels, authentication, audit logging, and file attachments are implemented. Current structure:
 
 ```
 internal/
   api/
-    handlers_audit.go       # Audit/completeness endpoints (implemented)
-    middleware.go            # Auth middleware (implemented)
+    audit_handlers.go       # Audit/completeness endpoints
+    auth_handlers.go        # Login, tokens, OIDC
+    bom_handlers.go         # Flat BOM, cost roll-up
+    file_handlers.go        # Presigned uploads, item files, thumbnails
+    handlers.go             # Items, schemas, projects, revisions
+    middleware.go            # Auth middleware
+    odoo_handlers.go        # Odoo integration endpoints
+    routes.go               # Route registration (75 endpoints)
+    search.go               # Fuzzy search
   auth/
-    auth.go                 # Auth service: local, LDAP, OIDC (implemented)
+    auth.go                 # Auth service: local, LDAP, OIDC
+  db/
+    items.go                # Item and revision repository
+    item_files.go           # File attachment repository
+    relationships.go        # BOM repository
+    projects.go             # Project repository
+  storage/
+    storage.go              # MinIO file storage helpers
 migrations/
-  008_odoo_integration.sql  # Odoo ERP tables (implemented)
-  009_auth.sql              # Auth + audit tables (implemented)
-  010_item_extended_fields.sql # Extended item fields (implemented)
+  001_initial.sql           # Core schema
+  ...
+  011_item_files.sql        # Item file attachments (latest)
 ```
 
 Future features would add:
@@ -371,13 +387,13 @@ Future features would add:
 ```
 internal/
   api/
-    handlers_lock.go        # Locking endpoints
+    lock_handlers.go        # Locking endpoints
   db/
     locks.go                # Lock repository
     releases.go             # Release repository
 migrations/
-  011_item_locks.sql        # Locking table
-  012_releases.sql          # Release management
+  012_item_locks.sql        # Locking table
+  013_releases.sql          # Release management
 ```
 
 ---
@@ -407,6 +423,18 @@ GET    /api/audit/completeness               # All items completeness summary
 GET    /api/audit/completeness/{partNumber}  # Per-item scoring
 ```
 
+**File Attachments (Implemented):**
+```
+GET    /api/auth/config                      # Auth config (public)
+POST   /api/uploads/presign                  # Presigned upload URL
+GET    /api/items/{pn}/files                 # List item files
+POST   /api/items/{pn}/files                 # Associate file with item
+DELETE /api/items/{pn}/files/{fileId}        # Delete file association
+PUT    /api/items/{pn}/thumbnail             # Set item thumbnail
+GET    /api/items/{pn}/bom/flat              # Flattened BOM
+GET    /api/items/{pn}/bom/cost              # Assembly cost roll-up
+```
+
 **Locking (Not Implemented):**
 ```
 POST   /api/items/{pn}/lock                 # Acquire lock