docs: document agent temp artifact cleanup and gitignore patterns (#261)

Add runbook guidance for deleting throwaway _encode/_emit/_inline commit
helpers after MCP commit attempts, ignore those patterns in .gitignore,
and cross-link the worktree-cleanup template.

Closes #261.

Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>

.gitignore

@@ -10,3 +10,7 @@ gitea-mcp*.json
 .vscode/
 graphify-out/
 branches/
+# Throwaway agent commit helpers (delete after MCP commit; see docs/llm-workflow-runbooks.md)
+/_encode_*.py
+/_emit_*.py
+/_inline_*.py

docs/llm-workflow-runbooks.md

@@ -370,6 +370,26 @@ git branch -d fix/issue-123-example
 All three helpers accept `--dry-run` to print the exact commands/paths without
 touching anything.
 
+### Agent temp artifact cleanup (#261)
+
+Failed or exploratory agent runs sometimes leave throwaway helper scripts in the
+repo root (for example `_encode_commit_payload.py`, `_emit_payload.py`,
+`_inline_commit.py`). These files are **not** part of any issue scope. They
+pollute `git status`, break `gitea_lock_issue`, and can trigger preflight
+fail-closed gates if created before `gitea_whoami`.
+
+**After every MCP commit attempt** (success or abort):
+
+1. Delete any root-level `_encode_*.py`, `_emit_*.py`, or `_inline_*.py` helpers
+   the agent created for payload preparation.
+2. Run `git status --porcelain` in the **author worktree** and confirm no
+   unexpected tracked or untracked files remain before `gitea_lock_issue`.
+3. Do not commit these helpers; stage only issue-scoped paths (`git add <files>`).
+
+The repo `.gitignore` ignores these patterns so accidental leftovers stay
+untracked. Ignored files still block issue-lock if they appear as tracked edits —
+delete them instead of leaving them in the tree.
+
 ### Create an issue / child issues
 
 - **Profile:** issue-manager or author (any profile allowed to create issues).

skills/llm-project-workflow/templates/worktree-cleanup.md

@@ -20,6 +20,8 @@ Steps:
    (removes branches/<type>-issue-<n>-<slug>; refuses if dirty; git branch -d is
    safe-delete only — fails on unmerged.)
 5. Delete the remote branch if the merge did not already remove it.
+5b. Delete any throwaway agent helpers (`_encode_*.py`, `_emit_*.py`, `_inline_*.py`)
+    left in the author worktree (see docs/llm-workflow-runbooks.md § Agent temp artifact cleanup).
 6. From the main checkout: git fetch <remote> --prune; git checkout master;
    git reset --hard <remote>/master ONLY if local master safely matches remote.
 7. Confirm main checkout clean and current (git status; 0 0 vs <remote>/master).