/fortify

name: fortify
description: Systematic ablation study runner. After research:run finds improvements, fortify identifies component candidates from git diff + diary, creates isolated git worktrees per ablation (main repo never modified), runs metric+guard in each worktree, ranks component importance, and optionally generates reviewer Q&A calibrated to a target venue.
argument-hint: '[<run-id>|<program.md>] [--venue <CVPR|NeurIPS|ICML|workshop>] [--max-ablations <N>] [--skip-run] [--keep "<items>"]'
effort: high
allowed-tools: Read, Write, Edit, Bash, Grep, Glob, Agent, TaskCreate, TaskUpdate, AskUserQuestion
disable-model-invocation: true

<objective>

Ablation study runner — after `/research:run` finds improvements, fortify identifies which components contributed, generates ablation variants (remove one component at a time), runs each in **isolated git worktrees** (main repo never modified), ranks component importance, optionally generates reviewer Q&A calibrated to venue.

NOT for: initial optimization loop (use `/research:run`); methodology validation (use `/research:judge`); paper-vs-code consistency (use `/research:verify`); hypothesis generation (use `research:scientist` directly). Fortify runs ablation studies on completed runs only.

</objective>

<constants>

MAX_ABLATION_CANDIDATES:  8 (ceiling — scientist produces 3–8; --max-ablations caps further)
METRIC_TIMEOUT_MS:        360000 (6 min — deliberately larger than run's 120s/300s VERIFY_TIMEOUT_SEC, to accommodate slower ablation-variant runs)
GUARD_TIMEOUT_MS:         360000
GIT_OP_TIMEOUT_MS:        15000
SANITY_DIVERGENCE_PCT:    2.0 (full-variant vs best_metric mismatch threshold)
IMPORTANCE_CLASS_CRITICAL: 50.0 (% of full metric lost)
IMPORTANCE_CLASS_SIGNIFICANT: 10.0
FORTIFY_DIR_BASE:         .experiments
STATE_DIR_BASE:           .experiments/state
METRIC_CMD_SOURCE:        state.json .config.metric_cmd (campaign's real metric — no fail-open default; env METRIC_CMD overrides)
GUARD_CMD_SOURCE:         state.json .config.guard_cmd (campaign's real guard — no fail-open default; env GUARD_CMD overrides)

</constants>

**Environment overrides** — set these before invoking the skill to override per-variant defaults:

• `METRIC_CMD` — command run inside each variant worktree to measure the ablation metric (override; default sourced from source-run `state.json` `.config.metric_cmd`)
• `GUARD_CMD` — command run inside each variant worktree to detect regressions (override; default sourced from source-run `state.json` `.config.guard_cmd`)
• `STATE_DIR_BASE` — base directory for source-run state lookups (default: `.experiments/state`)
• `FORTIFY_DIR_BASE` — base directory for per-run fortify artifacts (default: `.experiments`)

The constants block defaults above are YAML-only — bash blocks read environment variables (with `${VAR:-default}` fallback) and never source values directly from YAML.

<compaction>

• Key boundaries: end of F2 — ablation candidates identified by scientist; end of F4 — all ablation variant worktrees completed.
• Preserve at F2: FORTIFY_DIR (TMPDIR key), RUN_ID (TMPDIR key), ablation-candidates.jsonl path, best_metric from source run.
• Preserve at F4: FORTIFY_DIR, RUN_ID, results.jsonl path — ready for F5 importance ranking.
• F4 loop is resume-safe: 4a-init's resume guard skips variants already terminal (non-timeout) in results.jsonl, so a mid-loop compaction resumes at the first pending variant — never re-runs a completed ablation; a timed-out variant still retries.
• Clear at F1 start (stale prior run) and at start of F8 terminal summary.

</compaction>

<workflow>

<!-- Agent resolution: see _RESEARCH_SHARED/agent-resolution.md -->

Agent Resolution

**Agent resolution**: load and follow the protocol below. Contains foundry check + fallback table. If foundry not installed: use table to substitute each `foundry:X` with `general-purpose`. Agent this skill dispatches: `research:scientist` (same plugin — no fallback if research plugin installed).

# loads: compaction-contract.md
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
_RESEARCH_SHARED=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/resolve_shared.py" 2>/dev/null)  # timeout: 5000
[ -z "$_RESEARCH_SHARED" ] && { echo "! Plugin path resolution failed — ensure research plugin installed and CLAUDE_PLUGIN_ROOT set, or invoke /research:fortify from project root."; exit 1; }
echo "$_RESEARCH_SHARED" > "${TMPDIR:-/tmp}/research-shared-${CSID}"  # cold resolve — every later site reads this sentinel instead of re-running python
cat "$_RESEARCH_SHARED/agent-resolution.md"

| Agent | Fallback if absent | | -- | -- | | `research:scientist` | `general-purpose` (ablation candidate identification and reviewer Q&A quality reduced — **⚠ general-purpose agent may not emit the JSON envelope this skill parses; surface partial output and surface ⚠ in F7 report**) |

CRITICAL: Worktree-based isolation

**Do NOT use `git checkout -b <branch>` for ablations** — dirties main working tree, corrupts concurrent tool calls. Each ablation gets own git worktree under `$FORTIFY_DIR/worktrees/<variant>`, created from `best_commit`. Main working tree NEVER modified. Cleanup: `git worktree remove --force` per variant; `git worktree prune` on interrupt.

Fortify Mode (Steps F1–F8)

Triggered by `fortify` or `fortify <run-id|program.md>`.

**Task tracking**: create tasks for F1, F2, F3, F4, F5, F6, F7, F8 at start — before any tool calls.

Step F1: Locate source run, parse flags, and validate judge approval

Extract flags: `--venue <VENUE>`, `--max-ablations <N>`, `--skip-run`, `--keep "<items>"`.

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/extract-keep-flag.py" fortify "$ARGUMENTS" --venue-choices CVPR,NeurIPS,ICML,workshop  # timeout: 5000 — keep-items + venue sentinels; empty venue → F6 skip rule; exit 2 on an invalid venue

**Unsupported flag check**: load and fol