Fortify

<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 — same as run SKILL.md)
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-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
_RESEARCH_SHARED=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/resolve_shared.py" 2>/dev/null)  # timeout: 5000
[ -z "$_RESEARCH_SHARED" ] && { echo "! Plugin path resolution failed — ensure research plugin installed and CLAUDE_PLUGIN_ROOT set, or invoke /research:fortify from project root."; exit 1; }
cat "$_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>".

# Extract --keep quoted value (compaction-contract.md §keep semantics)
KEEP_ITEMS=""
if [[ "$ARGUMENTS" =~ --keep[[:space:]]\"([^\"]+)\" ]]; then
    KEEP_ITEMS="${BASH_REMATCH[1]}"
fi
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
# Clear stale contract from any prior incomplete run (compaction-contract.md §Lifecycle)
rm -f .temp/state/skill-contract.md  # timeout: 5000
echo "${KEEP_ITEMS:-}" > "${TMPDIR:-/tmp}/fortify-keep-items-${CSID}"  # persist for F2/F4 contract writes

Unsupported flag check: load and follow the protocol below. Supported flags for this skill: --venue, --max-ablations, --skip-run, --keep.

# loads: unsupported-flag-protocol.md
_RESEARCH_SHARED=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/resolve_shared.py" 2>/dev/null)  # timeout: 5000
cat "$_RESEARCH_SHARED/unsupported-flag-protocol.md"

Input resolution (priority order):

1. Explicit <run-id> argument → read $STATE_DIR_BASE/<run-id>/state.json
2. Explicit <program.md> argument → scan $STATE_DIR_BASE/*/state.json for matching program_file, pick latest with status: completed or status: goal-achieved
3. No argument → scan $STATE_DIR_BASE/, pick latest with status: completed or status: goal-achieved
4. None found → stop:

   fortify: No completed run found. Run /research:run first.
   

Initialize base directory bash variables (constants YAML is not auto-exported; environment overrides honored):

STATE_DIR_BASE="${STATE_DIR_BASE:-.experiments/state}"
FORTIFY_DIR_BASE="${FORTIFY_DIR_BASE:-.experiments}"

METRIC_CMD/GUARD_CMD are NOT defaulted here — they are sourced from the source-run state.json after $RUN_ID resolves (see block below). No fail-open default: git diff --stat HEAD always exits 0, so a defaulted guard would be a no-op that never catches ablation regressions.

Assign $RUN_ID from input resolution above (must be set before guard block uses it):

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
STATE_DIR_BASE="${STATE_DIR_BASE:-.experiments/state}"  # re-derive env default (Check 41: fresh shell)
_ARG1=$(echo "$ARGUMENTS" | awk '{print $1}')
if [ -n "$_ARG1" ] && [ "${_ARG1#-}" = "$_ARG1" ] && [ ! -f "$_ARG1" ] && [ -d "$STATE_DIR_BASE/$_ARG1" ]; then
  RUN_ID="$_ARG1"
elif [ -n "$_ARG1" ] && [ -f "$_ARG1" ]; then
  # program.md path — find latest completed run matching program_file  <!-- loads: find_run_id.py -->
  RUN_ID=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/find_run_id.py" "$STATE_DIR_BASE" --match-program "$_ARG1" 2>/dev/null)
else
  RUN_ID=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/find_run_id.py" "$STATE_DIR_BASE" 2>/dev/null)
fi
[ -z "$RUN_ID" ] && { echo "fortify: No completed run found. Run /research:run first."; exit 1; }
echo "$RUN_ID" > "${TMPDIR:-/tmp}/fortify-run-id-${CSID}"  # persist for later blocks (Check 41: fresh shell)

Source metric_cmd/guard_cmd from the campaign — env override first, then source-run state.json .config; fail closed if neither present (a defaulted git diff --stat HEAD guard always exits 0 → no-op that never catches regressions):

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
STATE_DIR_BASE="${STATE_DIR_BASE:-.experiments/state}"  # re-derive env default (Check 41: fresh shell)
IFS= read -r RUN_ID < "${TMPDIR:-/tmp}/fortify-run-id-${CSID}" 2>/dev/null || RUN_ID=""  # re-hydrate from F1 (Check 41)
STATE_JSON="$STATE_DIR_BASE/$RUN_ID/state.json"
METRIC_CMD="${METRIC_CMD:-$(jq -r '.config.metric_cmd // empty' "$STATE_JSON" 2>/dev/null)}"
GUARD_CMD="${GUARD_CMD:-$(jq -r '.config.guard_cmd // empty' "$STATE_JSON" 2>/dev/null)}"
if [ -z "$METRIC_CMD" ] || [ -z "$GUARD_CMD" ]; then
  echo "fortify: BLOCKED — $STATE_JSON .config missing metric_cmd/guard_cmd; ablation needs the campaign's real metric and guard commands."
  echo "Re-run /research:run to regenerate state.json, or set METRIC_CMD/GUARD_CMD in the environment."
  exit 1
fi
printf '%s' "$METRIC_CMD" > "${TMPDIR:-/tmp}/fortify-metric-cmd-${CSID}"  # persist for 4d (Check 41: fresh shell)
printf '%s' "$GUARD_CMD" > "${TMPDIR:-/tmp}/fortify-guard-cmd-${CSID}"    # persist for 4e (Check 41: fresh shell)

Guard: judge approval required. Judge skill writes verdict to .reports/research/judge-<branch>-<date>.md — scan for APPROVED verdict line:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
STATE_DIR_BASE="${STATE_DIR_BASE:-.experiments/state}"  # re-derive env default (Check 41: fresh shell)
IFS= read -r RUN_ID < "${TMPDIR:-/tmp}/fortify-run-id-${CSID}" 2>/dev/null || RUN_ID=""  # re-hydrate from F1 (Check 41)
JUDGE_VERDICT_FILE=$(ls -t .reports/research/judge-*.md 2>/dev/null | head -1)  # timeout: 5000
if [ -z "$JUDGE_VERDICT_FILE" ]; then
  echo "fortify: BLOCKED — no judge verdict found in .reports/research/."
  echo "Ablation studies require an approved baseline. Run: /research:judge <program.md>"
  exit 1
fi
JUDGE_VERDICT=$(grep -i '^[*]*[Vv]erdict[*]*:' "$JUDGE_VERDICT_FILE" | head -1 | sed 's/\*\*//g' | sed -E 's/.*[Vv]erdict[: ]+//' | sed 's/[[:space:]]*$//')  # strip trailing only; preserve internal spaces (e.g. "NEEDS REVISION")

PROGRAM_FILE=$(grep -iE '^[*]*(Program(_file)?|Program file)[*]*:' "$JUDGE_VERDICT_FILE" | head -1 | sed 's/\*\*//g' | sed -E 's/.*:[[:space:]]*//' | sed 's/[[:space:]]*$//')
# F-02 guard: empty PROGRAM_FILE means verdict lacks program metadata — cannot verify applicability
if [ -z "$PROGRAM_FILE" ]; then
    echo "fortify: BLOCKED — judge verdict missing Program: field; cannot verify verdict applies to current experiment."
    echo "Re-run: /research:judge <program.md> to generate a fresh verdict with required metadata."
    exit 1
fi
# Use explicit run-specific state.json path (resolved during F1 input resolution) — never CWD-relative
STATE_PROGRAM=$(jq -r '.program_file // ""' "$STATE_DIR_BASE/$RUN_ID/state.json" 2>/dev/null)
# Normalize both to absolute paths before comparing: judge report may store a relative program path while state.json stores absolute (run does realpath) — a raw string compare would false-BLOCK a matching program
_PF_ABS=$(realpath "$PROGRAM_FILE" 2>/dev/null || echo "$PROGRAM_FILE")
_SP_ABS=$(realpath "$STATE_PROGRAM" 2>/dev/null || echo "$STATE_PROGRAM")
if [ -n "$STATE_PROGRAM" ] && [ -n "$PROGRAM_FILE" ] && [ "$_PF_ABS" != "$_SP_ABS" ]; then
    printf "! BLOCKED — judge verdict references program '%s' but current experiment is for '%s'\n" "$PROGRAM_FILE" "$STATE_PROGRAM"
    printf "Run: /research:judge %s\n" "$STATE_PROGRAM"
    exit 1
fi
if [ -n "$PROGRAM_FILE" ] && [ ! -f "$PROGRAM_FILE" ]; then
    printf "! BLOCKED — program file %s referenced by judge verdict not found on disk\n" "$PROGRAM_FILE"
    exit 1
fi
echo "$PROGRAM_FILE" > "${TMPDIR:-/tmp}/fortify-program-file-${CSID}"  # persist for F6 reviewer-Q&A block (Check 41)

Verify JUDGE_VERDICT == "APPROVED". The program cross-match above guarantees the verdict was issued for the current experiment — fortify cannot ablate against a different program's verdict. Apply explicit bash gate — prose alone never halts execution:

JUDGE_VERDICT="${JUDGE_VERDICT:-REJECTED}"
if [ "$JUDGE_VERDICT" != "APPROVED" ]; then
    echo "fortify: BLOCKED — no APPROVED judge verdict found for this program."
    echo "Judge verdict: $JUDGE_VERDICT — stopping before implementation (F1–F7)."
    echo "Ablation studies require an approved baseline. Run: /research:judge <program.md>"
    exit 1
fi

Note: do NOT infer from methodology.md alone — methodology_rating: sound is one input to verdict, not verdict itself. Only ## Verdict line in judge output file is authoritative.

Read from state.json: goal, best_metric, best_commit, config (including metric_cmd, guard_cmd, compute), program_file.

Also read baseline_commit — iteration 0 commit from experiments.jsonl (first line, status: "baseline", field "commit").

Pre-compute run directory (each in separate Bash call):

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
FORTIFY_DIR=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/make_run_dir.py" "fortify" ".experiments" 2>/dev/null)  # timeout: 5000
[ -z "$FORTIFY_DIR" ] && { echo "! make_run_dir.py failed — ensure research plugin installed"; exit 1; }
mkdir -p "$FORTIFY_DIR"
echo "$FORTIFY_DIR" > "${TMPDIR:-/tmp}/fortify-dir-${CSID}"  # persist run dir for F2/F4-loop/F6 blocks (Check 41: make_run_dir non-idempotent)
WORKTREE_BASE="$FORTIFY_DIR/worktrees"
mkdir -p "$WORKTREE_BASE"
STATE_DIR="${STATE_DIR_BASE:-/tmp}/fortify-$(basename "$FORTIFY_DIR")"
mkdir -p "$STATE_DIR"

Step F2: Identify ablation candidates via scientist

Gather two inputs for scientist:

1. Git diff: run git diff <baseline_commit>...<best_commit> --stat (summary) and full git diff <baseline_commit>...<best_commit>. If full diff exceeds ~200 lines, write to $FORTIFY_DIR/diff.txt via Write tool; otherwise inline in prompt.
2. Experiment history: paths to experiments.jsonl and diary.md from source run directory.

Spawn research:scientist via Agent(subagent_type="research:scientist", prompt="...") with health monitoring (15-min cutoff, one 5-min extension — same pattern as judge J3).

Before building the prompt, substitute all bash variables into a single concrete string — never pass literal <FORTIFY_DIR> or <path> placeholders to the agent:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
STATE_DIR_BASE="${STATE_DIR_BASE:-.experiments/state}"  # re-derive env default (Check 41: fresh shell)
IFS= read -r RUN_ID < "${TMPDIR:-/tmp}/fortify-run-id-${CSID}" 2>/dev/null || RUN_ID=""  # re-hydrate from F1 (Check 41)
IFS= read -r FORTIFY_DIR < "${TMPDIR:-/tmp}/fortify-dir-${CSID}" 2>/dev/null || FORTIFY_DIR=""  # re-hydrate from F1 (Check 41)
EXPERIMENTS_PATH="$STATE_DIR_BASE/$RUN_ID/experiments.jsonl"
DIARY_PATH="$STATE_DIR_BASE/$RUN_ID/diary.md"
F2_PROMPT="Act as an ML ablation study designer.

Read:
- git diff at ${FORTIFY_DIR}/diff.txt (or inline if small)
- experiments.jsonl at ${EXPERIMENTS_PATH} (filter for entries with status: 'kept')
- diary.md at ${DIARY_PATH} (if exists)

Identify 3-8 distinct logical components that were changed during this run.
A component = a logically independent change that can be removed independently.

For each component produce one JSON line to ${FORTIFY_DIR}/ablation-candidates.jsonl:
{
  \"component_id\": <int>,
  \"name\": \"<descriptive name, e.g. 'learning rate warmup'>\",
  \"description\": \"<what it does and why it was introduced>\",
  \"files\": [\"<file:line range>\"],
  \"revert_commits\": [\"<commit SHA>\"],
  \"expected_importance\": \"HIGH|MEDIUM|LOW\"
}

Write your analysis to ${FORTIFY_DIR}/candidates-analysis.md.
Include ## Confidence block.
Return ONLY: {\"status\":\"done\",\"components\":N,\"file\":\"${FORTIFY_DIR}/ablation-candidates.jsonl\",\"confidence\":0.N}"

Pass $F2_PROMPT (fully expanded) as the prompt= argument to Agent(...).

Synchronous spawn note: the F2 scientist is spawned synchronously (not run_in_background=true), so CLAUDE.md §6 sentinel polling is unreachable mid-call. Timeout is handled post-hoc — after Agent() returns, check $FORTIFY_DIR/ablation-candidates.jsonl; if missing or empty, stop with "fortify: Scientist timed out. Check $FORTIFY_DIR/ for partial output." and surface with ⏱.

Read ablation-candidates.jsonl after scientist completes. If --max-ablations <M> specified and component count + 1 (for full variant) exceeds M: sort by expected_importance (HIGH first, then MEDIUM, then LOW), keep top M-1 components plus always include full sanity-check variant. Log dropped components: print a warning listing each dropped component by component_id and expected_importance so users can verify the scientist's importance estimates before proceeding. Include this list in the F7 report under ## Dropped Variants.

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
# Compaction contract — boundary 1: after F2 scientist completes, candidates ready (compaction-contract.md §Lifecycle)
IFS= read -r _RUN_ID < "${TMPDIR:-/tmp}/fortify-run-id-${CSID}" 2>/dev/null || _RUN_ID=""
IFS= read -r _FORTIFY_DIR < "${TMPDIR:-/tmp}/fortify-dir-${CSID}" 2>/dev/null || _FORTIFY_DIR=""
IFS= read -r _KEEP < "${TMPDIR:-/tmp}/fortify-keep-items-${CSID}" 2>/dev/null || _KEEP=""
_KEEP_APPEND=""; [ -n "$_KEEP" ] && _KEEP_APPEND="; user-keep: $_KEEP"
mkdir -p .temp/state  # timeout: 5000
{
    echo "## Active Skill Contract"
    echo "- skill: research:fortify · phase: ablation-execution (after F2 candidates identified)"
    echo "- run-dir: ${_FORTIFY_DIR}"
    echo "- preserve: run-id=${_RUN_ID}, fortify-dir=${_FORTIFY_DIR}, candidates=${_FORTIFY_DIR}/ablation-candidates.jsonl, variants=${_FORTIFY_DIR}/variants.jsonl${_KEEP_APPEND}"
    echo "- next: F3 generate variants → F4 run worktrees sequentially"
} > .temp/state/skill-contract.md  # timeout: 5000

--skip-run early exit: if --skip-run flag present, print candidate table (component_id, name, description, files, expected_importance) and exit. No ablation execution. Mark tasks F3, F4, F5, F6, F7 as skipped via TaskUpdate. Print all three lines (no .reports/research/fortify-*.md is written in --skip-run mode — only ablation-candidates.jsonl lives under $FORTIFY_DIR; surface $FORTIFY_DIR explicitly so the user can locate the candidate list):

fortify: --skip-run — <N> candidates identified.
Candidates artifact: $FORTIFY_DIR/ablation-candidates.jsonl
Next: /research:fortify without --skip-run to execute ablations

Jump to F8 (skip-run variant).

Step F3: Generate ablation variants

For each component from F2, one ablation variant: no-<component-name> (slugified — lowercase, spaces to hyphens). Plus one full variant (sanity check — should reproduce best_metric).

Write variant configs to $FORTIFY_DIR/variants.jsonl via Write tool — one JSON line per variant:

{"variant_name": "full", "component_removed": null, "revert_commits": [], "revert_strategy": "none"}
{"variant_name": "no-<name>", "component_removed": "<name>", "revert_commits": ["<sha1>", "<sha2>"], "revert_strategy": "git-revert"}

Step F4: Run ablation variants via worktrees

Run each variant sequentially — parallel worktrees would conflict.

Before loop — store original working directory and pre-create worktree-paths accumulator:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
ORIG_DIR="$(pwd)"  # timeout: 3000
echo "$ORIG_DIR" > "${TMPDIR:-/tmp}/fortify-orig-dir-${CSID}"  # persist for 4f cleanup cd (Check 41: fresh shell)
WORKTREE_PATHS_FILE=$(mktemp -t fortify-XXXX) || { echo "! BLOCKED — mktemp failed (tmpfs full or permission denied); cannot create cleanup accumulator. Aborting."; exit 1; }  # timeout: 3000
echo "$WORKTREE_PATHS_FILE" > "${TMPDIR:-/tmp}/fortify-paths-ptr-${CSID}"

# F-04: validate best_commit is a concrete SHA — `git worktree add` with a branch tip
# would advance the branch and pollute shared history on subsequent `git revert`.
if ! best_commit_sha=$(git rev-parse --verify "$best_commit^{commit}" 2>/dev/null); then
    echo "! BLOCKED — best_commit '$best_commit' does not resolve to a commit. Re-run source experiment or correct state.json."
    exit 1
fi
best_commit="$best_commit_sha"  # downstream `git worktree add` always sees a SHA → detached HEAD
echo "$best_commit" > "${TMPDIR:-/tmp}/fortify-best-commit-${CSID}"  # persist for 4a worktree-add (Check 41: fresh shell)

On interrupt (user abort or unexpected error mid-loop): cd "$ORIG_DIR" first, then git worktree prune (timeout: 15000) to clean up partially created worktrees before exiting. The trap below makes interrupt cleanup automatic — never rely on prose-only cleanup discipline.

For each variant in variants.jsonl:

4a-init. Derive VARIANT_NAME from the current iteration (must be set before any 4a/4b/4c/4d/4e block uses it):

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
VARIANT_NAME="variant-$(echo "$variant_spec" | jq -r '.variant_name' 2>/dev/null | tr ' ' '-' | tr '[:upper:]' '[:lower:]' | sed 's/^variant-//')"
# Fallback when variant_spec is just the bare name (not full JSON object) OR jq returned empty/null/error.
# Covers: empty (`variant-`), JSON null (`variant-null`), plain-text input that jq cannot parse.
if [ -z "$VARIANT_NAME" ] || [ "$VARIANT_NAME" = "variant-null" ] || [ "$VARIANT_NAME" = "variant-" ]; then
    VARIANT_NAME="variant-$(echo "${variant_spec:-unnamed}" | tr ' ' '-' | tr '[:upper:]' '[:lower:]' | sed 's/^variant-//')"
fi
# Final hard guard: after both attempts, VARIANT_NAME must be non-trivial (more than just "variant-").
if [ "$VARIANT_NAME" = "variant-" ] || [ -z "$VARIANT_NAME" ]; then
    echo "! BLOCKED — could not derive non-empty VARIANT_NAME from variant_spec; check variants.jsonl format. Skipping iteration."
    continue
fi
echo "$VARIANT_NAME" > "${TMPDIR:-/tmp}/fortify-variant-name-${CSID}"  # persist for 4a–4f blocks this iteration (Check 41: fresh shell)

4a-guard. Resume guard — skip variants already recorded terminal in results.jsonl:

# WHY: on mid-loop auto-compact + resume the F4 loop restarts from variant 1; without this guard each
# already-completed ablation (a full training run) re-executes. results.jsonl is the resume ledger.
# Match the un-prefixed name (4g/delta convention) tolerant of an optional "variant-" prefix; skip only
# NON-timeout terminal statuses so a transient timeout still retries on resume.
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r VARIANT_NAME < "${TMPDIR:-/tmp}/fortify-variant-name-${CSID}" 2>/dev/null || VARIANT_NAME=""  # re-hydrate (Check 41: fresh shell)
_VN_RAW="${VARIANT_NAME#variant-}"
IFS= read -r _FORTIFY_DIR < "${TMPDIR:-/tmp}/fortify-dir-${CSID}" 2>/dev/null || _FORTIFY_DIR=""; _RESULTS="$_FORTIFY_DIR/results.jsonl"
if [ -f "$_RESULTS" ] && grep -E "\"variant\":\"(variant-)?$_VN_RAW\"" "$_RESULTS" 2>/dev/null | grep -qE '"status":"(completed|revert-conflict|revert-missing|metric-failed)"'; then
    echo "→ $_VN_RAW already terminal (non-timeout) in results.jsonl — skipping (resume)"
    continue
fi

4a. Create isolated worktree at best_commit:

# Re-hydrate WORKTREE_BASE/VARIANT_NAME/best_commit inline (Check 41: fresh shell; inline keeps `git` as first token for allow-list match; CSID inlined per-substitution — same reason)
git worktree add "$(cat "${TMPDIR:-/tmp}/fortify-dir-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)/worktrees/$(cat "${TMPDIR:-/tmp}/fortify-variant-name-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)" "$(cat "${TMPDIR:-/tmp}/fortify-best-commit-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)"  # timeout: 15000

4a-trap. Register cleanup trap immediately after worktree creation (guarantees removal on EXIT / INT / TERM, even on uncaught error):

# Reload (Check 41: shell var lost between Bash calls)
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r WORKTREE_PATHS_FILE < "${TMPDIR:-/tmp}/fortify-paths-ptr-${CSID}" 2>/dev/null || WORKTREE_PATHS_FILE=""
[ -z "$WORKTREE_PATHS_FILE" ] && WORKTREE_PATHS_FILE="${TMPDIR:-/tmp}/fortify-worktree-paths-fallback-${CSID}"
IFS= read -r FORTIFY_DIR < "${TMPDIR:-/tmp}/fortify-dir-${CSID}" 2>/dev/null || FORTIFY_DIR=""; WORKTREE_BASE="$FORTIFY_DIR/worktrees"  # re-hydrate (Check 41: fresh shell)
IFS= read -r VARIANT_NAME < "${TMPDIR:-/tmp}/fortify-variant-name-${CSID}" 2>/dev/null || VARIANT_NAME=""  # re-hydrate (Check 41: fresh shell)
WORKTREE_PATH="${FORTIFY_WORKTREE:-$WORKTREE_BASE/$VARIANT_NAME}"
echo "$WORKTREE_PATH" >> "$WORKTREE_PATHS_FILE"  # accumulator file persists across Bash calls; array vars do not
trap 'while IFS= read -r _wt; do git worktree remove --force "$_wt" 2>/dev/null; done < "$WORKTREE_PATHS_FILE" 2>/dev/null; rm -f "$WORKTREE_PATHS_FILE"' EXIT INT TERM

The accumulator file ($WORKTREE_PATHS_FILE) is pre-created via mktemp before the variant loop begins. Each variant appends its path and re-registers the trap to cover all paths added so far. The explicit git worktree remove in 4f remains for happy-path cleanup; the trap is a safety net for interrupted loops only. mktemp ensures collision-free naming across concurrent invocations.

4b. Navigate into worktree (two separate Bash calls — cd first, then command):

# Re-hydrate WORKTREE_BASE/VARIANT_NAME inline (Check 41: fresh shell; inline keeps `cd` as first token; CSID inlined per-substitution — same reason)
cd "$(cat "${TMPDIR:-/tmp}/fortify-dir-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)/worktrees/$(cat "${TMPDIR:-/tmp}/fortify-variant-name-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)"  # timeout: 3000

4c. Apply revert (skip for full variant):

For full variant: no changes — proceed to 4d.

For no-<component> variant: revert component's commits.

IMPORTANT — order matters: revert in reverse chronological order (newest first) to avoid conflicts. If revert_commits from variants.jsonl is chronological (oldest first), reverse before reverting.

Bash call 1 — extract and sort revert_commits via jq + awk (no python; jq-based JSONL filter avoids per-iteration approval prompt):

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r FORTIFY_DIR < "${TMPDIR:-/tmp}/fortify-dir-${CSID}" 2>/dev/null || FORTIFY_DIR=""  # re-hydrate (Check 41: fresh shell)
IFS= read -r VARIANT_NAME < "${TMPDIR:-/tmp}/fortify-variant-name-${CSID}" 2>/dev/null || VARIANT_NAME=""  # re-hydrate (Check 41: fresh shell)
REVERT_COMMITS_RAW=$(jq -r --arg vn "$VARIANT_NAME" 'select(.variant_name==$vn) | .revert_commits[]' "$FORTIFY_DIR/variants.jsonl" 2>/dev/null | tr '\n' ' ')  # timeout: 5000
[ -z "$REVERT_COMMITS_RAW" ] && { echo "⚠ No revert_commits for $VARIANT_NAME — skipping"; echo '{"variant":"'$VARIANT_NAME'","status":"revert-missing"}' >> "$FORTIFY_DIR/results.jsonl"; continue; }
# Sort newest-first for conflict-free revert (portable awk reverse — tac not on macOS)
REVERT_COMMITS_SORTED=$(echo "$REVERT_COMMITS_RAW" | tr ' ' '\n' | awk '{lines[NR]=$0} END{for(i=NR;i>=1;i--) print lines[i]}' | tr '\n' ' ')
echo "$REVERT_COMMITS_SORTED" > "${TMPDIR:-/tmp}/fortify-revert-sorted-${CSID}"  # persist for git-revert block (Check 41: fresh shell)

Bash call 2 — apply revert (separated so first-token allow-list matches git):

# Re-hydrate REVERT_COMMITS_SORTED inline (Check 41: fresh shell; unquoted for multi-SHA word-splitting; inline keeps `git` first token; CSID inlined per-substitution — same reason)
git revert $(cat "${TMPDIR:-/tmp}/fortify-revert-sorted-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null) --no-edit  # timeout: 15000

If revert produces merge conflicts: append {"variant":"<name>","status":"revert-conflict",...} to results.jsonl, jump to 4f (cleanup).

4d. Run metric_cmd in worktree:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r METRIC_CMD < "${TMPDIR:-/tmp}/fortify-metric-cmd-${CSID}" 2>/dev/null || METRIC_CMD=""  # re-hydrate from F1 (Check 41: fresh shell)
[ -z "$METRIC_CMD" ] && { echo "fortify: BLOCKED — metric_cmd not initialized in F1"; exit 1; }
$METRIC_CMD  # timeout: 360000  (sourced from state.json .config.metric_cmd in F1)
METRIC_EXIT=$?

Parse stdout for numeric metric value. If command fails or no numeric output: record status: "metric-failed", jump to 4f.

4e. Run guard_cmd in worktree:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r GUARD_CMD < "${TMPDIR:-/tmp}/fortify-guard-cmd-${CSID}" 2>/dev/null || GUARD_CMD=""  # re-hydrate from F1 (Check 41: fresh shell)
[ -z "$GUARD_CMD" ] && { echo "fortify: BLOCKED — guard_cmd not initialized in F1"; exit 1; }
$GUARD_CMD  # timeout: 360000  (sourced from state.json .config.guard_cmd in F1)
GUARD_EXIT=$?

Record guard result: "pass" (exit 0) or "fail" (non-zero).

4f. Cleanup worktree (INVARIANT — must execute even if 4c/4d/4e fail):

# Re-hydrate ORIG_DIR inline (Check 41: fresh shell; inline keeps `cd` as first token; CSID inlined per-substitution — same reason)
cd "$(cat "${TMPDIR:-/tmp}/fortify-orig-dir-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)"  # timeout: 3000

# Re-hydrate WORKTREE_BASE/VARIANT_NAME inline (Check 41: fresh shell; inline keeps `git` as first token; CSID inlined per-substitution — same reason)
git worktree remove --force "$(cat "${TMPDIR:-/tmp}/fortify-dir-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)/worktrees/$(cat "${TMPDIR:-/tmp}/fortify-variant-name-${CLAUDE_CODE_SESSION_ID:-$PPID}" 2>/dev/null)"  # timeout: 15000

4g. Record result — append one JSON line to $FORTIFY_DIR/results.jsonl:

{"variant":"<name>","component_removed":"<name or null>","metric":0.0,"delta_from_full":0.0,"delta_pct":0.0,"guard":"pass|fail","status":"completed|revert-conflict|metric-failed|timeout","timestamp":"<ISO>"}

delta_from_full and delta_pct are placeholders — computed in post-loop step below.

After all variants processed:

git worktree prune  # timeout: 15000

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
# Compaction contract — boundary 2: after F4 all variants complete (compaction-contract.md §Lifecycle)
IFS= read -r _RUN_ID < "${TMPDIR:-/tmp}/fortify-run-id-${CSID}" 2>/dev/null || _RUN_ID=""
IFS= read -r _FORTIFY_DIR < "${TMPDIR:-/tmp}/fortify-dir-${CSID}" 2>/dev/null || _FORTIFY_DIR=""
IFS= read -r _KEEP < "${TMPDIR:-/tmp}/fortify-keep-items-${CSID}" 2>/dev/null || _KEEP=""
_KEEP_APPEND=""; [ -n "$_KEEP" ] && _KEEP_APPEND="; user-keep: $_KEEP"
mkdir -p .temp/state  # timeout: 5000
{
    echo "## Active Skill Contract"
    echo "- skill: research:fortify · phase: post-ablation (after F4 worktrees complete)"
    echo "- run-dir: ${_FORTIFY_DIR}"
    echo "- preserve: run-id=${_RUN_ID}, fortify-dir=${_FORTIFY_DIR}, results=${_FORTIFY_DIR}/results.jsonl${_KEEP_APPEND}"
    echo "- next: F5 rank importance → F6 reviewer Q&A → F7 report"
} > .temp/state/skill-contract.md  # timeout: 5000

Post-loop delta computation: read results.jsonl, find full variant metric. For each completed no-<component> variant:

• delta_from_full = ablated_metric - full_metric
• delta_pct = (delta_from_full / abs(full_metric)) * 100 (signed — negative means removing component hurt). If full_metric == 0: set delta_pct = 0 (avoid division by zero).

Update results.jsonl with computed deltas via Write tool (rewrite full file).

Step F5: Rank component importance

For each no-<component> variant with status: "completed":

• Read metric_direction from ## Metric block in program_file (higher or lower). If absent, default to higher.

• Compute signed delta (positive = removal hurt metric → component helpful):

  signed_delta = (full_metric - ablated_metric) * (1 if direction == 'higher' else -1)
  importance = signed_delta / abs(full_metric) * 100 if full_metric != 0 else 0
  

• Importance class (helpful components — signed_delta >= 0):

  • CRITICAL: importance > 50%
  • SIGNIFICANT: importance 10–50%
  • MARGINAL: importance < 10% Sign convention check — after computing signed_delta for all variants, verify:

• For direction == 'higher': all helpful components should have signed_delta >= 0 (ablated metric < full)

• For direction == 'lower': all helpful components should have signed_delta >= 0 (ablated metric > full; removing component worsened metric)

• Any component where signed_delta has unexpected sign: flag explicitly in report as "sign anomaly — verify ablation ran correctly"

• Potentially Harmful class: signed_delta < -5% — removing component IMPROVED metric. Surface in dedicated Potentially Harmful Components report section; not ranked in main table.

Borderline components (CI spans zero): if a confidence interval is available and spans zero (includes both positive and negative values), do NOT classify as MARGINAL. Instead:

• Add to a "Borderline Components" subsection in the F7 report
• Note: "CI spans zero — component may be neutral or harmful; additional runs required before including in model"
• Do not rank these in the main importance table; surface separately

Coupling check — before sorting, scan the ablation candidates (from ablation-candidates.jsonl) for notes on architectural dependencies. For any pair where one component explicitly requires the other (noted in description field or candidates-analysis.md):

• Mark both components in the ranking with [COUPLED] suffix
• Add a note: "Independent ablation unreliable — recommend joint ablation of [A + B]"
• Add to the "Skipped Variants" section: joint-[A]-[B] — not run (joint ablation recommended)
• Surface as a ! WARNING in the F7 report before the ranking table

Sort by importance descending (helpful components only). Write to $FORTIFY_DIR/importance-ranking.json via Write tool — JSON array with fields: rank, component, full_metric, ablated_metric, signed_delta_pct, importance_pct, class (CRITICAL/SIGNIFICANT/MARGINAL/HARMFUL).

Sanity check: compare full variant metric against best_metric from state.json. If divergence exceeds 2%:

Warning: Sanity check failed: full-variant metric=<X> differs from best_metric=<Y> by <Z>%. Results may be unreliable (non-deterministic metric or environment change).

Include warning prominently in F7 report.

Step F6: Reviewer Q&A (optional — --venue only)

Skip entirely if no --venue flag. Supported venues: CVPR, NeurIPS, ICML, workshop.

Spawn research:scientist via Agent(subagent_type="research:scientist", prompt="..."). Synchronous spawn note: spawned synchronously (not run_in_background=true) — CLAUDE.md §6 sentinel polling is unreachable mid-call. After Agent() returns, check $FORTIFY_DIR/reviewer-qa.md; if missing or empty, treat as timed out and surface with ⏱.

Before building the prompt, substitute all bash variables into a single concrete string — never pass literal <FORTIFY_DIR>, <path>, or <venue> placeholders to the agent:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
VENUE="${VENUE:-workshop}"  # parsed from --venue flag in F1
IFS= read -r PROGRAM_FILE < "${TMPDIR:-/tmp}/fortify-program-file-${CSID}" 2>/dev/null || PROGRAM_FILE=""  # re-hydrate from F1 (Check 41: fresh shell)
IFS= read -r FORTIFY_DIR < "${TMPDIR:-/tmp}/fortify-dir-${CSID}" 2>/dev/null || FORTIFY_DIR=""  # re-hydrate from F1 (Check 41: fresh shell)
[ -z "$PROGRAM_FILE" ] && { echo "! fortify: BLOCKED — PROGRAM_FILE not set; re-invoke from F1"; exit 1; }  # absolute path resolved in F1
F6_PROMPT="Act as a peer reviewer for ${VENUE}.

Read:
- ablation results at ${FORTIFY_DIR}/results.jsonl
- importance ranking at ${FORTIFY_DIR}/importance-ranking.json
- original program.md at ${PROGRAM_FILE}

Generate:
1. 5-7 likely reviewer questions calibrated to ${VENUE} standards
   (CVPR/NeurIPS/ICML: expect thorough ablations, statistical significance, compute budget justification; workshop: lighter bar)
2. For each question: a data-backed answer referencing specific ablation results
3. A supplementary material draft section with the ablation table (LaTeX-ready)

Write to ${FORTIFY_DIR}/reviewer-qa.md.
Include ## Confidence block.
Return ONLY: {\"status\":\"done\",\"questions\":N,\"file\":\"${FORTIFY_DIR}/reviewer-qa.md\",\"confidence\":0.N}"

Pass $F6_PROMPT (fully expanded) as the prompt= argument to Agent(...).

Health monitoring: same as F2 (15-min cutoff, one extension). On timeout: note "Reviewer Q&A: timed out" in report, continue to F7.

Step F7: Write fortify report

Pre-compute branch if not already set:

BRANCH=$(git branch --show-current 2>/dev/null | tr '/' '-' || echo 'main')  # timeout: 3000

mkdir -p .reports/research  # timeout: 3000

Write full report to .reports/research/fortify-$BRANCH-$(date +%Y-%m-%d).md via Write tool. Anti-overwrite: BASE=".reports/research/fortify-$BRANCH-$(date +%Y-%m-%d).md"; OUT="$BASE"; COUNT=2; while [ -f "$OUT" ]; do OUT="${BASE%.md}-${COUNT}.md"; ((COUNT++)); done

---
Fortify — [goal]
Date:        [YYYY-MM-DD]
Scope:       [run-id] / [N] components identified
Focus:       ablation study / component importance ranking
Agents:      research:scientist (F2, F6)
Outcome:     [N] critical · [N] significant · [N] marginal components
Top:         [component-name] (importance: X.X% · CRITICAL|SIGNIFICANT|MARGINAL)
Confidence:  [score] — [key gaps]
Next steps:  simplify by removing marginal components, re-run /research:run
Path:        → .reports/research/fortify-<branch>-<date>.md
---

## Fortify Report: <goal>

**Source run**: <run-id>
**Date**: <date>
**Baseline commit**: <best_commit>
**Components identified**: <N>
**Ablations run**: <N completed> of <N+1 planned>

### Sanity Check (full variant)
Full metric: <value> (expected from run: <best_metric>) — PASS | Warning MISMATCH (<Z>% divergence)

### Component Importance Ranking

| Rank | Component | Full Metric | Ablated Metric | Signed Δ | Importance | Class |
|------|-----------|-------------|----------------|----------|------------|-------|
| 1    | ...       | ...         | ...            | +X.X%    | X.X%       | CRITICAL |

### Potentially Harmful or Borderline Components

Components that either:
- Improved the metric when removed (`signed_delta < -5%`) — **Potentially Harmful**
- Have CI spanning zero — **Borderline** (insufficient evidence of contribution)

| Component | Full Metric | Ablated Metric | Signed Δ | Status |
|-----------|-------------|----------------|----------|--------|
| ...       | ...         | ...            | -X.X%    | Potentially Harmful |
| ...       | ...         | CI [−a, +b]    | n/a      | Borderline |

(Omit section entirely if no harmful or borderline components found.)

### Ablation Matrix

| Variant       | Metric | Guard | Status           | Delta from Full |
|---------------|--------|-------|------------------|-----------------|
| full          | ...    | pass  | completed        | baseline        |
| no-component1 | ...    | pass  | completed        | -X.X%           |
| no-component2 | ...    | n/a   | revert-conflict  | n/a             |

### Skipped Variants
<list any revert-conflict, metric-failed, or timeout variants with reason>

### Reviewer Q&A
<section from F6 if --venue was specified; otherwise omit this section entirely>

Full artifacts: <FORTIFY_DIR>/

## Confidence
**Score**: 0.N — [high|moderate|low]
**Gaps**:
- [specific limitation]

Step F8: Terminal summary

rm -f .temp/state/skill-contract.md  # clear contract — fortify complete (compaction-contract.md §Lifecycle)  # timeout: 5000

Print compact terminal summary:

---
Fortify — <goal>
Source run:   <run-id>
Sanity:       full=<value> (expected <best_metric>) — PASS | Warning MISMATCH
Components:   <N> identified · <N> ablations completed
Top:          <component-name> (importance: X.X% · CRITICAL|SIGNIFICANT|MARGINAL)
Marginal:     <N> components < 10% each
Venue Q&A:    generated for <venue> | n/a
-> saved to .reports/research/fortify-<branch>-<date>.md
-> ablation artifacts: <FORTIFY_DIR>/
---
Next: simplify model by removing marginal components, re-run /research:run

If --skip-run used (early exit at F2): replace ablation lines with:

---
Fortify — <goal> (--skip-run)
Source run:   <run-id>
Components:   <N> candidates identified — ablations not executed
-> candidates: <FORTIFY_DIR>/ablation-candidates.jsonl
-> analysis:   <FORTIFY_DIR>/candidates-analysis.md
---
Next: run /research:fortify without --skip-run to execute ablations

</workflow> <calibration>

Calibratable: F1–F3 sub-steps only — synthetic ablation plan with known component importance order; score whether fortify correctly ranks components and identifies reviewer questions. Full F4–F6 execution loop (worktree creation, metric runs, real guard scripts) excluded — requires live git state and metric commands.

See the domain table entry for /research:fortify for the full ground-truth checklist. Path resolution:

_FOUNDRY_CALIBRATE=$(ls -td ~/.claude/plugins/cache/borda-ai-rig/foundry/*/skills/calibrate/modes 2>/dev/null | head -1); [ -z "$_FOUNDRY_CALIBRATE" ] && _FOUNDRY_CALIBRATE="plugins/cc_foundry/skills/calibrate/modes"
# See: $_FOUNDRY_CALIBRATE/skills.md

</calibration> <notes>

• Worktree invariant — cleanup (git worktree remove --force) must run even if metric/guard fails. No stale worktrees. Final git worktree prune catches missed cleanup.
• Main repo never modified — all ablation work in worktrees. Main working tree stays clean.
• Sequential execution — variants run one at a time. Parallel worktrees would require separate detached HEADs and complicate cleanup.
• No compound Bash commands — always two separate Bash calls (cd then command). CWD persists between calls.
• Bash tool timeout parameter — never shell timeout wrapper. Pass timeout: <ms> on Bash tool call.
• Judge prerequisite — fortify refuses without APPROVED judge verdict. Prevents ablation on unapproved methodologies.
• --skip-run for planning — generates candidate list without running ablations. Useful for reviewing what would be ablated before committing compute.
• --skip-run scope: flag skips ablation execution only — source run (research:run) must already be complete. Does not affect source run.
• Fortify run directories don't write result.jsonl — exempt from 30-day TTL cleanup (no result.jsonl = cleanup skipped); remove manually when done (rm -rf .experiments/fortify-*/)
• Compute mode: local execution only. --compute and --colab passthrough not implemented — contributions welcome. Until then, fortify runs metric_cmd/guard_cmd directly in each worktree on local machine.
• Revert conflicts expected — when commits interleave (component A's commit touches same lines as B's), revert may conflict. Recorded as revert-conflict, not treated as error.

</notes>