investigate

Diagnose unknown failures: broken local setup, environment mismatch, tool misbehavior, hook problems, CI vs local divergence, permission errors, runtime anomalies. Gather signals broadly, eliminate hypotheses systematically, report confirmed root cause + recommended next skill. No fixes — diagnosis only. NOT for: known Python test failures with traceback (use /develop:debug (requires develop plugin)); .claude/ config quality sweep (use /foundry:audit).

• $ARGUMENTS: required — symptom, question, or failing command, e.g.:

  • "hooks not firing on Save"
  • "bridge review is unavailable on this machine"
  • "/calibrate times out every run"
  • "CI fails but passes locally"
  • "uv run pytest can't find conftest.py"

• --fast: optional flag — skip Step 4 adversarial Codex review; use when speed matters more than thoroughness or Codex unavailable.

If $ARGUMENTS empty or too vague, use AskUserQuestion: "What exactly is failing or behaving unexpectedly? Include the command and any error output you can share."

Task hygiene: load and follow the protocol below.

# loads: compaction-contract.md
# audit-skip: resilience-replication
python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_foundry}/bin/load_shared_doc.py" foundry skills/_shared task-hygiene.md  # timeout: 5000

Task tracking: TaskCreate tasks for Gather, Hypothesise, Probe, Report; mark in_progress/completed as you go.

Step 1: Parse symptom and scope

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
KEEP_ITEMS=""
if [[ "$ARGUMENTS" =~ --keep[[:space:]]\"([^\"]+)\" ]]; then
    KEEP_ITEMS="${BASH_REMATCH[1]}"
fi
ARGUMENTS=$(echo "$ARGUMENTS" | sed 's/--keep "[^"]*"//g')
rm -f .temp/state/skill-contract.md ${TMPDIR:-/tmp}/investigate-verdicts-${CSID}  # clear stale contract + probe ledger (compaction-contract.md §Lifecycle)  # timeout: 5000
echo "$KEEP_ITEMS" > "${TMPDIR:-/tmp}/investigate-keep-items-${CSID}"

From $ARGUMENTS extract:

• What: specific failure or anomaly
• Where: local / CI / both; which tool or command; which skill or hook if applicable
• When: started recently (after change) or always broken; intermittent or consistent

Unsupported flag check — after all supported flags extracted (--fast, --keep), scan $ARGUMENTS for remaining --<token> tokens. If found: print ! Unknown flag(s): `--<token>`. Supported: `--fast`, `--keep`. then invoke AskUserQuestion — (a) Abort (stop, re-invoke with correct flags) · (b) Continue ignoring (skip unknown flags, proceed). On Abort: stop.

Step 2: Gather signals

Init run directory unconditionally at start of Step 2 — $INVESTIGATE_RUN must be set even when Step 4 skipped (--fast path), so Step 6's read of $INVESTIGATE_RUN/*-review.md does not expand to /codex-review.md or unset reference. Step 4 creates review files only when adversarial review runs; Step 6 must guard reads with [ -f <path> ].

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
# timeout: 5000
INVESTIGATE_RUN=".temp/investigate/$(date -u +%Y-%m-%dT%H-%M-%SZ)"
mkdir -p "$INVESTIGATE_RUN"
echo "$INVESTIGATE_RUN" > "${TMPDIR:-/tmp}/investigate-run-path-${CSID}"  # persist; re-read in later steps
echo "INVESTIGATE_RUN=$INVESTIGATE_RUN"  # bash vars don't persist; read from stdout

Collect evidence in parallel — do NOT form hypotheses yet. Tool versions and PATH:

which python && python --version                                                                   # timeout: 5000
which uv 2>/dev/null && uv --version 2>/dev/null || echo "uv: not found"                             # timeout: 5000
node --version 2>/dev/null || echo "node: not found"                                                 # timeout: 5000
CODEX_STATUS=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_foundry}/bin/check_bridge.py" --status 2>/dev/null || echo "absent"); echo "bridge@borda-ai-rig: $CODEX_STATUS"  # timeout: 5000

env | grep -E 'PATH|VIRTUAL_ENV|UV_|CLAUDE|HOME|SHELL|NODE' | grep -v -E '(_TOKEN|_KEY|_SECRET|_PASSWORD|_PASS)=' | sort # timeout: 5000

Recent changes:

git log --oneline -10        # timeout: 3000
git diff HEAD~3..HEAD --stat # timeout: 3000

Config state (when symptom involves Claude Code, hooks, or skills):

Use Read to check .claude/settings.json — look for hook registrations, allow entries relevant to failing command, and enabledMcpjsonServers. For ~/.claude/settings.json (outside allowed Read paths), use Bash:

jq . ~/.claude/settings.json  # timeout: 5000

Logs (when symptom involves skill run, background agent, or hook):

Use Grep with pattern ERROR|WARN|failed|not found|exit across .notes/logs/, .claude/logs/ (legacy fallback), /tmp/, or relevant .reports/<skill>/ run dirs. Read last 50 lines of any relevant log file.

Capture all output before Step 3.

After gathering evidence, capture top signals as working notes for Step 4 spawn prompts AND persist them to disk so the values survive the bash-state reset between Steps 2 → 3 → 4:

• SYMPTOM_DESCRIPTION — verbatim from $ARGUMENTS
• KEY_SIGNALS — write 3–5 bullet-point sentences summarizing the most diagnostic signals found above (tool versions, missing binaries, config anomalies, recent changes)

Use the Write tool (NOT a echo > $INVESTIGATE_RUN/... heredoc, which loses bash variable state across tool calls) to write the captured values to disk so Step 4 spawn prompts can instruct subagents to Read them rather than relying on inline interpolation:

• Write(file_path="<INVESTIGATE_RUN>/symptom.txt", content=<SYMPTOM_DESCRIPTION>) — substitute <INVESTIGATE_RUN> with the path printed in the Step 2 bash output above
• Write(file_path="<INVESTIGATE_RUN>/signals.md", content=<KEY_SIGNALS>)

Step 4 spawn prompts must instruct the subagent to Read these files (not rely on inline ${SYMPTOM_DESCRIPTION} interpolation, which the LLM can paraphrase or truncate under context pressure).

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r _INVESTIGATE_RUN < "${TMPDIR:-/tmp}/investigate-run-path-${CSID}" 2>/dev/null || _INVESTIGATE_RUN=""
IFS= read -r _KEEP < "${TMPDIR:-/tmp}/investigate-keep-items-${CSID}" 2>/dev/null || _KEEP=""
_PRESERVE="run-dir=$_INVESTIGATE_RUN, symptom=$_INVESTIGATE_RUN/symptom.txt, signals=$_INVESTIGATE_RUN/signals.md"
[ -n "$_KEEP" ] && _PRESERVE="$_PRESERVE; user-keep: $_KEEP"
mkdir -p .temp/state  # timeout: 5000
{
    echo "## Active Skill Contract"
    echo "- skill: foundry:investigate · phase: hypothesise+probe (after signal gather)"
    echo "- run-dir: $_INVESTIGATE_RUN"
    echo "- preserve: $_PRESERVE"
    echo "- next: rank hypotheses (Step 3) → adversarial review (Step 4) → probe (Step 5) → report (Step 6)"
} > .temp/state/skill-contract.md

Step 3: Rank hypotheses

List candidate root causes ranked by probability, drawing only from gathered evidence:

Rank	Hypothesis	Supporting evidence	Ruling-out test
1	…	…	…
2	…	…	…
3	…	…	…

Capture the ranked hypothesis table as HYPOTHESIS_TABLE and persist it to disk before Step 4 — use the Write tool:

• Write(file_path="<INVESTIGATE_RUN>/hypotheses.md", content=<HYPOTHESIS_TABLE>)

This avoids LLM-paraphrase risk when inlining a long table into a spawn prompt. Step 4 spawn prompts will instruct the subagent to Read this file.

Refresh the compaction contract now that ranking is done — the boundary moves into the Step 4–5 loop so a mid-loop compaction resumes from hypotheses.md instead of re-ranking:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
# Compaction contract — boundary 2: ranking done, entering adversarial+probe loop (compaction-contract.md §Lifecycle)
IFS= read -r _IR < "${TMPDIR:-/tmp}/investigate-run-path-${CSID}" 2>/dev/null || _IR=""
IFS= read -r _KEEP < "${TMPDIR:-/tmp}/investigate-keep-items-${CSID}" 2>/dev/null || _KEEP=""
_PRESERVE="run-dir=$_IR, symptom=$_IR/symptom.txt, signals=$_IR/signals.md, hypotheses=$_IR/hypotheses.md"
[ -n "$_KEEP" ] && _PRESERVE="$_PRESERVE; user-keep: $_KEEP"
mkdir -p .temp/state  # timeout: 5000
{
    echo "## Active Skill Contract"
    echo "- skill: foundry:investigate · phase: adversarial+probe (after hypotheses ranked)"
    echo "- run-dir: $_IR"
    echo "- preserve: $_PRESERVE"
    echo "- next: adversarial review (Step 4, unless --fast) → probe hypotheses (Step 5) → report (Step 6). Resume from hypotheses.md — do NOT re-rank."
} > .temp/state/skill-contract.md

Common categories:

• Environment mismatch — tool version differs; wrong virtualenv active; PATH missing entry
• Missing dependency — binary not on PATH; package not installed; module import fails
• Config / permission error — settings.json allow entry missing; hook path wrong; settings.local.json override
• State pollution — stale lock file, leftover tmp artifact, or cached state conflicts with current run
• Recent change regression — git commit or config edit introduced issue (check git log)
• Sync drift — project .claude/ and ~/.claude/ diverged; compare manually or /foundry:audit setup
• External service — network unavailable, API rate-limited, or remote tool unreachable

Step 4: Auxiliary review (optional)

Skip entirely when --fast passed, or top hypothesis has strong direct evidence. (foundry:challenger is always available as part of foundry plugin, so the skip condition simplifies to: skip when --fast passed.) Skip → proceed to Step 5.

When --fast: mark Step 4 task as deleted (not completed — it was skipped).

Otherwise, set up adversarial review. Run dir created in Step 2; re-resolve path string here (bash state does not persist):

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
# timeout: 5000
IFS= read -r INVESTIGATE_RUN < "${TMPDIR:-/tmp}/investigate-run-path-${CSID}" 2>/dev/null || INVESTIGATE_RUN=""
# fallback if path file absent
[ -z "$INVESTIGATE_RUN" ] && INVESTIGATE_RUN=$(find .temp/investigate -maxdepth 1 -mindepth 1 -type d 2>/dev/null | sort -Vr | head -1)
CODEX_OUT="$INVESTIGATE_RUN/codex-review.md"
echo "INVESTIGATE_RUN=$INVESTIGATE_RUN"
echo "CODEX_OUT=$CODEX_OUT"  # spawn-prompt reads both stdout lines

Step 2 appends the resolved run path to ${TMPDIR:-/tmp}/investigate-run-path-${CSID} so this resolution succeeds — see echo "$INVESTIGATE_RUN" > "${TMPDIR:-/tmp}/investigate-run-path-${CSID}" in Step 2.

Re-check Codex availability at point of use (bash vars don't persist across tool calls) and echo result so next prose decision can read it:

# check_bridge.py resolves the installed-and-enabled state in one call and already honors a
# project-local .claude/settings.json opt-out, which an inline registry read does not.
CODEX_STATUS=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_foundry}/bin/check_bridge.py" --status 2>/dev/null || echo "absent")  # timeout: 5000
[ "$CODEX_STATUS" = "available" ] && CODEX_AVAILABLE=true || CODEX_AVAILABLE=false
[ "$CODEX_AVAILABLE" = "false" ] && printf "  bridge@borda-ai-rig is %s — skipping bridge review\n" "$CODEX_STATUS"
echo "CODEX_AVAILABLE=$CODEX_AVAILABLE"  # bash vars don't persist; branch below MUST read this value from stdout

Read CODEX_AVAILABLE=… from bash stdout above (NOT shell state). Printed true: spawn Codex; else spawn foundry:challenger. Spawn prompts below instruct subagent to Read persisted symptom/signals/hypotheses files (written in Steps 2 and 3) — more reliable than inlining values, which the LLM can paraphrase under context pressure.

If the bridge is available (requires bridge@borda-ai-rig installed and enabled) — substitute concrete path strings for <INVESTIGATE_RUN> and <CODEX_OUT> before constructing the prompt:

Agent budget — each spawn costs ~120,851 tok of fixed overhead (~73 tool-calls' worth) plus ~12.0 s/call, so work under ~73 calls is cheaper done inline: spawn nothing. Keep each agent near ~55 tool-calls; past ~60 they stall without returning an envelope, forcing reconstruction from disk. Every spawn prompt must require an envelope even on exhaustion — partial: true plus what was finished.

Skill(skill="bridge:review", args="Read-only adversarial review of hypothesis quality. Read <INVESTIGATE_RUN>/symptom.txt, <INVESTIGATE_RUN>/signals.md, and <INVESTIGATE_RUN>/hypotheses.md. Challenge the top hypothesis, identify blind spots, and surface alternative root causes. Write full findings to <CODEX_OUT> and return a compact result envelope.")

Else (Codex unavailable) — substitute <INVESTIGATE_RUN> with the printed run-dir path:

Agent(subagent_type="foundry:challenger", prompt="Adversarial review of hypothesis quality. Read these files for full context: <INVESTIGATE_RUN>/symptom.txt, <INVESTIGATE_RUN>/signals.md, <INVESTIGATE_RUN>/hypotheses.md. Challenge the top hypothesis, identify blindspots, and surface alternative root causes. Read-only analysis only. Write full findings to <INVESTIGATE_RUN>/challenger-review.md using the Write tool. Return ONLY: {\"status\":\"done\",\"file\":\"<path>\",\"findings\":N,\"severity\":{\"critical\":N,\"high\":N,\"medium\":N,\"low\":N},\"confidence\":0.N,\"summary\":\"<one-line>\"}")

Before issuing the call: scan constructed prompt string for remaining < or > characters — if present, substitution incomplete; resolve before spawning.

• Add challenger alternative hypotheses as new rows in Step 3 table
• Re-rank if challenger gives stronger evidence for lower-ranked candidate
• If challenger finds category not in common list, add it

Step 5: Probe top hypotheses

One targeted test per hypothesis — clear confirm/rule-out signal. Run independent probes in parallel.

# Example probes — adapt to the actual symptom

# Environment mismatch
python --version  # timeout: 3000

# Missing allow entry
jq -r '.permissions.allow[]' ~/.claude/settings.json

# Hook path wrong
ls -la ~/.claude/hooks/

# Sync drift
diff <(jq -S . .claude/settings.json) <(jq -S . ~/.claude/settings.json) | head -40

Per probe: mark Confirmed, Ruled out, or Inconclusive. Append each verdict to the probe ledger and refresh the contract — so a mid-loop compaction does not re-probe an already-decided hypothesis:

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
# WHY: probe verdicts live only in-context; a post-compact resume without this would re-probe ruled-out hypotheses (loop)
echo "<hypothesis> :: <Confirmed|Ruled-out|Inconclusive>" >> ${TMPDIR:-/tmp}/investigate-verdicts-${CSID}
IFS= read -r _IR < "${TMPDIR:-/tmp}/investigate-run-path-${CSID}" 2>/dev/null || _IR=""
_VERDICTS=$(tail -8 "${TMPDIR:-/tmp}/investigate-verdicts-${CSID}" 2>/dev/null)  # cap keeps contract compact; tail keeps most-recent verdicts
_REVIEW=""; [ -f "$_IR/codex-review.md" ] && _REVIEW="$_IR/codex-review.md"; [ -f "$_IR/challenger-review.md" ] && _REVIEW="$_IR/challenger-review.md"
mkdir -p .temp/state  # timeout: 5000
{
    echo "## Active Skill Contract"
    echo "- skill: foundry:investigate · phase: probe (Step 5)"
    echo "- run-dir: $_IR"
    echo "- preserve: hypotheses=$_IR/hypotheses.md${_REVIEW:+, review=$_REVIEW}"
    if [ -n "$_VERDICTS" ]; then
        echo "- probed (do NOT re-probe):"
        echo "$_VERDICTS" | sed 's/^/    - /'
    fi
    echo "- next: probe remaining pending hypotheses → confirm root cause → report (Step 6). Skip Confirmed/Ruled-out above."
} > .temp/state/skill-contract.md

Stop when one hypothesis confirmed with clear evidence, or top-3 all ruled out (expand to lower-ranked candidates).

Step 6: Report findings

Re-resolve $INVESTIGATE_RUN from persisted path file (cat "${TMPDIR:-/tmp}/investigate-run-path-${CSID}"). Guard each read with [ -f <path> ]: if $INVESTIGATE_RUN/codex-review.md exists, read it; if $INVESTIGATE_RUN/challenger-review.md exists, read it. Either or both may be absent (Step 4 skipped via --fast, or spawned agent failed silently). Incorporate new hypotheses or blindspots from existing files into Evidence section below; skip read entirely if neither file present — do NOT block on missing review files.

## Investigation: <symptom>

**Root cause**: <confirmed cause, or "inconclusive — suspects narrowed to X, Y">

**Evidence**:
- <key finding that confirmed the diagnosis>
- <secondary supporting evidence>

**Ruled out**: <hypotheses eliminated and why>

**Recommended next action**: <one of:>
  - `/develop:fix` — code regression confirmed (application code only — NOT for `.claude/` changes) (requires `develop` plugin — check plugin availability before following this recommendation)
  - `/foundry:manage update <name> "<change directive>"` — `.claude/` agent/skill content needs adding or updating (NOT for structural/quality sweeps — use `/foundry:audit` for that)
  - `/foundry:audit` — structural/quality issue in `.claude/` config confirmed (e.g. broken cross-refs, missing blocks, tag imbalance); NOT for content additions — use `/manage update` for those
  - `/foundry:setup` — propagate project `.claude/` to `~/.claude/` (foundry plugin is the distribution path)
  - Manual step: <exact command to run>
  - Further investigation needed: <what additional info would resolve it>

End with a ## Confidence block:

## Confidence
**Score**: 0.N — [high ≥0.9 | moderate 0.85–0.9 | low <0.85 ⚠]
**Gaps**:
- [e.g., root cause unconfirmed — probe was inconclusive; external service logs inaccessible]

**Refinements**: N passes.
- Pass 1: [gap addressed]

Invoke AskUserQuestion as follow-up gate: (a) Invoke recommended next action (from Recommended next action field above) (b) Run additional investigation with narrowed hypothesis (c) Skip — diagnosis complete

export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
rm -f .temp/state/skill-contract.md ${TMPDIR:-/tmp}/investigate-verdicts-${CSID}  # clear contract + probe ledger — skill complete (compaction-contract.md §Lifecycle)  # timeout: 5000

• Diagnosis only — never apply fixes; hand off with specific recommended action
• Scope vs /develop:debug: /develop:debug (requires develop plugin) needs known test failure, runs TDD fix loop. /investigate = "something wrong, don't know what" — cause may not be in application code
• Scope vs /foundry:audit: /foundry:audit = scheduled quality sweep of .claude/. /investigate = triggered by live failure; two complement each other (investigate finds config symptom → audit confirms structural issue)
• Follow-up: /develop:fix (requires develop plugin) for implementing resolution once root cause confirmed
• Broad first: always complete Step 2 before hypothesising — premature anchoring = most common investigation failure
• Parallel probes: run independent probes in single response, avoid serial latency
• Inconclusiveness valid: report what ruled out and what info would close remaining gap — don't fabricate root cause to appear decisive
• Root-cause discipline: drill to confirmed root cause before handoff — never hand off "likely cause"; if fix applied and symptoms persist, re-invoke investigate with residual symptom to continue the loop; full protocol in rules/debugging.md