All tool calls must follow the exact API described in the MCP server documentation. If a required tool is unavailable, you **MUST** log the error and stop execution.
### Tool call format (CRITICAL)
Tool calls **MUST** use this exact XML format — no spaces inside the angle brackets:
Each time processing fails, we increment the counter (write the new number).
If after increment the counter < 3, we keep the line in the task file.
If counter reaches 3, we **remove the line from the task file**, add it to `docs/failed/phase1/internal/align/align.go.failed` (just a marker), and log the error.
If the description could apply to any project, it is INVALID. You MUST include domain‑specific context (bioinformatics, sequence processing, etc.) and concrete behaviour.
- Use `find pkg -name "*.go" ! -name "*_test.go" ! -path "*/cmd/*"` to list all Go files (excluding tests and main.go).
- Write the list (one relative path per line, e.g., `internal/align/align.go`) to `docs/todo/phase1.txt`.
3. Do the same for phase2 and phase3 later when those phases start.
4.**No other state is stored.**
---
# Phase 1: File documentation
**Processing rule:**
- Read the **first line** of `docs/todo/phase1.txt` (using `head -n 1`).
- If the file is empty, Phase 1 is complete → proceed to Phase 1bis initialization.
- Otherwise, process that single file.
**Processing a file:**
1. Let `relpath` be the line content (e.g., `internal/align/align.go`).
2. Check if a permanent failure marker exists at `docs/failed/phase1/${relpath}.failed`. If yes, remove the line from the task file and skip (line will be deleted).
3. If the documentation file `docs/phase1/${relpath}.go.md` exists go directly to its validation (step 6).
4. Otherwise, generate documentation for that file (using MCP tools as before).
5. Write the documentation to `docs/phase1/${relpath}.go.md`.
6. Validate quality.
7. If validation succeeds:
- Remove the line from the task file.
- Remove any retry counter file for this item.
- (No sentinel needed; the removal from todo indicates completion.)
8. If validation fails:
- Increment retry counter:
- If `docs/retry/phase1/${relpath}.count` does not exist, set to 1.
- Else read it, add 1, write back.
- If new counter >= 3:
- Remove line from task file.
- Create `docs/failed/phase1/${relpath}.failed`.
- Log error.
- If new counter < 3:
- Keep the line in the task file (do nothing, it stays as first line for next run).
9.**Exit** (or stop if this was a single run). The next invocation will read the first line again (same if retry, or next if removed).
**Important:**
- Do **not** read more than one line.
- Do **not** attempt to process multiple items in one run.
- The LLM should finish after handling one item.
---
# Phase 1bis: Review and harmonization
When Phase 1 is complete (i.e., `docs/todo/phase1.txt` empty), we initialize `docs/todo/phase1bis.txt` with the same list of files (the ones that succeeded).
But note: we need to know which files were successfully documented. Since we removed lines from `phase1.txt` on success, we need a record. The simplest is to reuse the same list but we can generate it by listing the existing `.go.md` files in `docs/phase1/` (since every successful file has a `.go.md`).
Thus, Phase 1bis initialization:
- If `docs/todo/phase1bis.txt` does not exist, create it by listing all `.go.md` files under `docs/phase1/`, stripping the `docs/phase1/` prefix and the `.go.md` suffix, and writing the relative path (same format as phase1).
Then processing is identical to Phase 1, but using `docs/todo/phase1bis.txt` and output is overwriting the same `.go.md` files (with improvements). Retry counters go in `docs/retry/phase1bis/`.
