Refactor autopilot workflows and documentation: Update .gitignore to include binary and media file types, enhance agent command references in documentation, and modify annotation class for improved accessibility. Adjust inference processing to handle batch sizes and streamline test specifications for clarity and consistency across the system.

.cursor/skills/autopilot/SKILL.md

@@ -60,7 +60,7 @@ Every invocation follows this sequence:
 3. Cross-check state file against _docs/ folder structure (rules in state.md)
 4. Resolve flow (see Flow Resolution above)
 5. Resolve current step (detection rules from the active flow file)
-6. Present Status Summary (format in protocols.md)
+6. Present Status Summary (template in active flow file)
 7. Execute:
    a. Delegate to current skill (see Skill Delegation below)
    b. If skill returns FAILED → apply Skill Failure Retry Protocol (see protocols.md):
@@ -102,37 +102,6 @@ This skill activates when the user wants to:
 - User wants to document an existing codebase → use `/document` directly
 - User wants the full guided workflow → use `/autopilot`
 
-## Methodology Quick Reference
+## Flow Reference
 
-```
-┌────────────────────────────────────────────────────────────────┐
-│              Autopilot (Auto-Chain Orchestrator)                │
-├────────────────────────────────────────────────────────────────┤
-│ EVERY INVOCATION:                                              │
-│   1. Read state file + module files                            │
-│   2. Resolve flow & current step                               │
-│   3. Status Summary → Execute → Auto-chain (loop)             │
-│                                                                │
-│ GREENFIELD FLOW (flows/greenfield.md):                         │
-│   Step 0 Problem → Step 1 Research → Step 2 Plan              │
-│   → 2a UI Design (if UI) → Step 3 Decompose → [SESSION]     │
-│   → Step 4 Implement → Step 5 Run Tests                      │
-│   → 5b Security (opt) → 5c Perf Test (opt) → Step 6 Deploy  │
-│   → DONE                                                      │
-│                                                                │
-│ EXISTING CODE FLOW (flows/existing-code.md):                   │
-│   Pre-Step Document → 2b Test Spec → 2c Decompose Tests      │
-│   → [SESSION] → 2d Implement Tests → 2e Refactor             │
-│   → 2ea UI Design (if UI) → 2f New Task → [SESSION]         │
-│   → 2g Implement → 2h Run Tests → 2hb Security (opt)        │
-│   → 2hc Perf Test (opt) → 2i Deploy → DONE                  │
-│                                                                │
-│ STATE: _docs/_autopilot_state.md (see state.md)                │
-│ PROTOCOLS: choice format, Jira auth, errors (see protocols.md) │
-│ PAUSE POINTS: sub-skill BLOCKING gates only                    │
-│ SESSION BREAK: after Decompose/New Task (before Implement)     │
-├────────────────────────────────────────────────────────────────┤
-│ Auto-chain · State to file · Rich re-entry · Delegate          │
-│ Pause at decisions only · Minimize interruptions               │
-└────────────────────────────────────────────────────────────────┘
-```
+See `flows/greenfield.md` and `flows/existing-code.md` for step tables, detection rules, auto-chain rules, and status summary templates.