Fix FDT being overwritten #54

.agents/skills/fix-and-pr/SKILL.md

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+---
+name: fix-and-pr
+description: Reproduce, debug, fix, verify, and submit GBOS/Eonix kernel issues as pull requests. Use for kernel bug fixing, headless QEMU reproduction scripts, subagent-driven root-cause analysis, commit preparation, and credential-safe PR creation.
+---
+
+# GBOS / Eonix Fix and PR
+
+## Mandatory credential gate
+
+Run this before **any** other action: preflight, branch creation, issue
+fetching, builds, analysis, or subagent launches.
+
+1. Check `GH_TOKEN` without printing it:
+
+   ```bash
+   test -n "${GH_TOKEN:-}"
+   ```
+
+2. If the check succeeds, continue.
+3. If `GH_TOKEN` is unset or empty, stop immediately. Ask the user for a GitHub
+   token, preferably by exporting it:
+
+   ```text
+   GH_TOKEN is not set. Please provide a GitHub token by exporting it in your
+   shell, for example:
+     export GH_TOKEN='...'
+   Tell me when it is set; I will not continue until then.
+   ```
+
+4. Do not run tools, inspect the repository, spawn subagents, or begin the
+   workflow until the user confirms it is available and the check succeeds.
+5. Never echo, log, commit, or put `GH_TOKEN` in a subagent prompt. Do not
+   write it to a file.
+
+The detailed protocol is split by phase under `references/`. Read
+`references/README.md`, then `references/00-operating-contract.md`, then the
+document for the current phase. Load only the documents needed for that phase.
+
+If the task is not a GBOS/Eonix kernel issue, keep the same phase gates but
+replace repository-specific paths, build commands, and remotes.
+
+## When this skill applies
+
+- A GitHub issue, bug report, stack trace, or failing test must be reproduced
+  and fixed.
+- A QEMU-based kernel reproduction script is needed.
+- The work needs subagent orchestration for analysis, implementation, review,
+  or PR publication.
+- The user asks to prepare commits or open a PR for a verified fix.
+
+## Entry point
+
+```bash
+ISSUE=<issue-id>
+SLUG=<short-slug>
+BASE=<base-branch>
+ART="build/work/issue-${ISSUE}"
+mkdir -p "$ART"
+```
+
+Then:
+
+1. Confirm the credential gate above passes.
+2. Read `references/README.md` and `references/00-operating-contract.md`.
+3. Run the repository preflight in `references/01-environment-and-intake.md`.
+4. Capture the issue in `$ART/issue.json`.
+5. Follow the phase gates below in order, loading the matching reference
+   document when entering each phase.
+
+## Phase gates
+
+| Phase | Required evidence | Reference document |
+| --- | --- | --- |
+| 0. Intake and environment | `GH_TOKEN` present; clean checkout, configured toolchain, successful build, target QEMU boot, issue details captured. | [01 — Environment and issue intake](references/01-environment-and-intake.md) |
+| 1. Reproduction | Headless script independently verified to distinguish bug from fixed behavior. | [02 — Automated reproduction](references/02-reproduction.md) |
+| 2. Analysis | Root cause stated with evidence; fix boundary and invariants recorded. | [03 — Root-cause analysis](references/03-analysis.md) |
+| 3. Fix and commits | Minimal scoped fix; clean, independently buildable commits with repository-style messages. | [04 — Fix planning and implementation](references/04-fix-and-commits.md), [05 — Commit conventions](references/05-commit-conventions.md) |
+| 4. Verification and review | Baseline `--expect bug` passes, fixed `--expect fixed` passes, builds/tests pass, independent review has no blockers. | [06 — Verification and review](references/06-verification.md) |
+| 5. PR | Correct base/head, pushed branch, PR body with verification evidence, local and PR diffs match, no secrets. | [07 — PR submission](references/07-pr-submission.md) |
+
+Do not advance because a plausible fix exists. Advance only when the gate
+evidence exists.
+
+## Critical rules
+
+1. **One writer per worktree.** Never run concurrent writers in the same
+   checkout.
+2. **No reproduction, no fix.** Do not implement a speculative fix.
+3. **No post-fix verification, no PR.** The same reproducer must pass in fixed
+   mode after the fix.
+4. **Never use `git add -A` or `git add .`.** Add explicit paths only.
+5. **Never leak `GH_TOKEN`.** Do not print it, pass it in prompts, write it to
+   disk, embed it in URLs, or commit it.
+6. **Keep the fix minimal.** No unrelated refactors, formatting sweeps, or
+   dependency updates.
+7. **Separate authoring from review.** Use a fresh-context `reviewer` for the
+   independent diff review.
+8. **Stop on ambiguity.** Ask before changing unspecified behavior or choosing
+   a PR base branch.
+
+## Reproduction contract
+
+Save the script at:
+
+```text
+script/repro/issue-<id>-<slug>.exp
+```
+
+It must support:
+
+```text
+--expect bug|fixed
+--arch <arch>
+--mode <mode>
+--smp <n>
+--timeout <seconds>
+--log <path>
+--help
+```
+
+Exit codes:
+
+| Code | Meaning |
+| --- | --- |
+| `0` | Observed behavior matched `--expect` |
+| `1` | Observed behavior contradicted `--expect` |
+| `2` | Infrastructure failure |
+| `3` | Usage error |
+| `130` | Interrupted |
+
+Use `make test-run` for headless execution. Give QEMU a unique name and kill
+only that instance; never use global `killall qemu-system-*`.
+
+Before trusting the script, have a fresh verifier confirm:
+
+- `--expect bug` exits 0 on the unmodified tree.
+- `--expect fixed` exits 1 on the unmodified tree (negative control).
+- No QEMU process remains after any exit path.
+- Logs contain no secrets and are bounded.
+
+## Supporting references
+
+- [08 — Failure handling](references/08-failure-handling.md)
+- [09 — Issue analysis template](references/09-analysis-template.md)
+- [10 — Quick command reference](references/10-command-reference.md)
+- [11 — Prompt hygiene](references/11-prompt-hygiene.md)
+
+## Artifacts
+
+Keep issue state outside chat history:
+
+```text
+build/work/issue-<id>/
+├── issue.json
+├── analysis.md
+├── plan.md
+├── script-review.md
+├── before.log
+├── after.log
+└── pr.md
+```
+
+`build/` is ignored by Git, but `make clean` deletes it. Preserve important logs
+elsewhere before a clean rebuild.
+
+## Subagent roles
+
+| Role | Use |
+| --- | --- |
+| `scout` | Read-only issue intake, code mapping, log analysis, hypothesis generation. |
+| `worker` | One bounded implementation or script-generation task in one worktree. |
+| `reviewer` | Fresh-context challenge of the reproduction script, root cause, plan, or final diff. |
+| Publisher `worker` | Push the verified branch and create the PR; no code changes. |
+
+The supervisor retains phase-gate decisions, final diff ownership, and
+publication authority.
+
+## Output expectations
+
+When reporting progress or completion, include:
+
+- Issue id and chosen base/head branches.
+- Root cause and changed files.
+- Baseline and fixed reproduction results with log paths.
+- Build/test commands and exit codes.
+- Independent review verdict.
+- Commit hashes and PR URL, if created.
+- Remaining risks or blockers.
+
+READ ALL REFERENCE DOCUMENTATIONS UNDER THIS SKILL'S references/ DIRECTORY BEFORE CONTINUING!

.agents/skills/fix-and-pr/references/00-operating-contract.md

@@ -0,0 +1,121 @@
+# 00 — Operating contract
+
+Part of the GBOS/Eonix `fix-and-pr` skill.
+
+A standardized, end-to-end workflow for reproducing kernel issues, finding the
+root cause, implementing and verifying a fix, and opening a pull request with
+subagents.
+
+The workflow is deliberately **evidence-gated**. Do not advance to the next
+phase because a plausible fix exists; advance only when the previous phase has
+produced verifiable evidence.
+
+---
+
+## 0. Operating contract
+
+### 0.1 Roles
+
+| Role | Owner | Responsibility |
+| --- | --- | --- |
+| Supervisor | Parent agent | Owns issue interpretation, phase gates, final diff, commits, and PR. Resolves ambiguity and approves publication. |
+| Scout | `scout` subagent (read-only) | Fetches issue context, maps code paths, collects logs, proposes hypotheses. |
+| Worker | `worker` subagent (writer) | Implements one bounded change in one worktree. |
+| Reviewer | `reviewer` subagent (read-only, fresh context) | Independently challenges the reproduction script, diff, or root cause. |
+| Verifier | `worker` or `reviewer` with a test-only mandate | Runs the reproduction and builds; does not edit kernel code. |
+| Publisher | `worker` subagent | Pushes the branch and creates the PR. Does not change code. |
+
+The supervisor may perform any step directly when that is cheaper than
+delegation. Subagents are used to obtain isolation, independent verification,
+and parallelism, not as ceremony.
+
+### 0.2 Mandatory credential gate
+
+Before any other workflow action, check `GH_TOKEN` without printing it:
+
+```bash
+test -n "${GH_TOKEN:-}"
+```
+
+- If it is set and non-empty, continue.
+- If it is unset or empty, stop and ask the user for the token. Prefer asking
+  them to export it in their shell:
+
+  ```text
+  GH_TOKEN is not set. Please provide a GitHub token by exporting it:
+    export GH_TOKEN='...'
+  Tell me when it is set; I will not continue until then.
+  ```
+
+- Do not inspect the repository, fetch issues, build, spawn subagents, or begin
+  any phase until the user confirms it is available and the check succeeds.
+- Never echo, log, commit, or put `GH_TOKEN` in a prompt. Do not write it to a
+  file.
+
+### 0.3 Non-negotiable rules
+
+1. **One writer per worktree.** Never let two subagents edit the same checkout
+   concurrently.
+2. **No fix without reproduction.** If the issue cannot be reproduced, record
+   why and stop; do not implement a speculative fix.
+3. **No PR without post-fix verification.** The same reproduction that failed
+   before the fix must pass after it.
+4. **Separate evidence from authority.** A subagent report is evidence. The
+   supervisor decides whether it is sufficient.
+5. **Never leak credentials.** `GH_TOKEN` is read from the environment only.
+   Never print it, put it in a URL, a prompt, a commit, a log, or a file.
+6. **Never use `git add -A` or `git add .`.** Explicitly add intended files;
+   otherwise an untracked secret or log can enter the commit.
+7. **Minimal scope.** No unrelated refactors, formatting sweeps, or speculative
+   improvements in a bug-fix PR.
+8. **Stop on ambiguity.** Ask before changing behavior that is not clearly
+   required by the issue, or when the target base branch is unclear.
+
+### 0.4 Phase gates
+
+| Phase | Gate to leave the phase |
+| --- | --- |
+| 0. Intake and environment | `GH_TOKEN` is present; repository builds, target architecture runs, issue details captured. |
+| 1. Reproduction | A headless script exists and has been independently verified to distinguish bug from fixed behavior. |
+| 2. Analysis | Root cause is stated with evidence; the fix boundary is identified. |
+| 3. Fix and commits | Minimal fix is implemented; commits are clean and build independently. |
+| 4. Verification and review | Reproduction passes in fixed mode, baseline passes in bug mode, builds/tests pass, independent review has no blocking findings. |
+| 5. PR | Branch is pushed, PR is created with the correct base/head and verification evidence, and the local diff matches the PR diff. |
+
+### 0.5 Persistent artifacts
+
+Use issue-specific paths so later subagents can resume without relying on chat
+history:
+
+```bash
+ISSUE=123
+SLUG=short-issue-slug
+ART="build/work/issue-${ISSUE}"
+mkdir -p "$ART"
+```
+
+```text
+build/work/issue-<id>/
+├── issue.json              # issue metadata and comments, if fetched
+├── analysis.md             # observations, hypotheses, root cause
+├── plan.md                 # fix plan and test matrix
+├── script-review.md        # independent reproduction-script verdict
+├── before.log              # --expect bug run on the unmodified tree
+├── after.log               # --expect fixed run on the fixed tree
+└── pr.md                   # final PR title/body and URL
+```
+
+Reproduction scripts belong in `script/repro/`, because they may be reused by
+later subagents and optionally committed as regression tests:
+
+```text
+script/repro/issue-<id>-<slug>.exp
+```
+
+`build/` is ignored by Git, but `make clean` deletes it. Copy important logs
+out before a clean rebuild, or keep the canonical logs in a temporary directory
+such as `/tmp/gbos-issue-<id>/`.
+
+---
+
+Next: [01 — Environment and issue intake](01-environment-and-intake.md)