@jaggerxtrm/specialists 3.17.0 → 3.18.1

package/docs/archive/spec-v3.md

@@ -0,0 +1,792 @@
+---
+title: Specialists v3 — Implementation Specification
+scope: spec-v3
+category: reference
+version: 1.0.0
+updated: 2026-03-19
+domain: []
+---
+
+<!-- INDEX: auto-generated by validate_doc.py — do not edit manually -->
+| Section | Summary |
+|---|---|
+| [1. Architecture Overview](#1-architecture-overview) | Problem: N poll calls per run |
+| [2. File Layout](#2-file-layout) | On completion, status changes to "done" and elapsed_s is final |
+| [3. CLI Commands](#3-cli-commands) | **Foreground (default, existing behavior)**: Streams pi output to stdout in real time |
+| [4. Pi Subprocess Protocol](#4-pi-subprocess-protocol) | **--append-system-prompt**: The specialist's prompt |
+| [5. Schema Changes (.specialist.yaml)](#5-schema-changes-specialistyaml) | skills |
+| [6. Hook Notification](#6-hook-notification) | File: ~/ |
+| [7. PiAgentSession Changes](#7-piagentsession-changes) | Changes: |
+| [8. SpecialistRunner Changes](#8-specialistrunner-changes) | SpecialistRunner |
+| [9. MCP Server Changes](#9-mcp-server-changes) | **specialist_init**: Unchanged |
+| [10. Operational Concerns](#10-operational-concerns) | `specialists init` must add ` |
+| [11. Migration Path](#11-migration-path) | 1 |
+| [12. Testing Strategy](#12-testing-strategy) | - Supervisor lifecycle: mock PiAgentSession, verify status |
+| [13. Verification Checklist](#13-verification-checklist) | All items verified against pi-mono source (packages/coding-agent) and pi --help output |
+<!-- END INDEX -->
+
+# Specialists v3 — Implementation Specification
+
+> **Status**: Final spec. Ready for implementation.
+> **Date**: 2026-03-11
+> **Context**: This spec supersedes the file-backed registry + RpcClient plan from restructure.md.
+> **Core decision**: CLI is the execution plane. MCP is the control plane. Bash background jobs replace MCP async polling.
+
+---
+
+## 1. Architecture Overview
+
+### Current (v2)
+
+```
+Claude ──MCP──▶ start_specialist ──▶ PiAgentSession (subprocess)
+Claude ──MCP──▶ poll_specialist  ──▶ JobRegistry (in-memory) ──▶ delta + status
+Claude ──MCP──▶ poll_specialist  ──▶ ...repeat N times...
+Claude ──MCP──▶ poll_specialist  ──▶ status: done, full output
+```
+
+Problem: N poll calls per run. Each is a visible tool use. Thinking tokens, tool markers,
+and text deltas streamed into context window on every poll. 60-second specialist = 30+ tool
+calls, tens of thousands of wasted context tokens.
+
+### Target (v3)
+
+```
+Claude ──Bash──▶ specialists run overthinker --prompt "..." --background
+                   └▶ spawns pi --mode rpc (supervisor stays alive)
+                   └▶ writes status.json on lifecycle events
+                   └▶ writes events.jsonl (lifecycle + tool events only)
+                   └▶ on agent_end: queries get_last_assistant_text → result.txt
+                   └▶ queries get_state → session path → session.txt
+                   └▶ closes stdin → pi exits → supervisor exits
+
+Claude ──Bash──▶ specialists status                    (one-liner per job, ~30 tokens)
+Claude ──Bash──▶ specialists result <id>               (full output, once, when done)
+Claude ──Bash──▶ specialists run X --continue <id> --prompt "..."   (multi-turn)
+```
+
+Hook notification (optional): UserPromptSubmit hook checks .specialists/jobs/*/status.json
+for newly completed jobs, injects one-line banner on next user prompt.
+
+### MCP Role (reduced)
+
+MCP server retains: specialist_init, list_specialists, specialist_status (circuit breaker
+health), use_specialist (quick synchronous tasks). The async job tools (start_specialist,
+poll_specialist, stop_specialist, run_parallel) are deprecated — their functionality moves
+to CLI commands.
+
+---
+
+## 2. File Layout
+
+```
+.specialists/                          # project root, parallel to .beads/
+  jobs/
+    <job-id>/
+      status.json                      # overwritten on every lifecycle event
+      events.jsonl                     # append-only lifecycle + tool events
+      result.txt                       # written once on agent_end (clean assistant text)
+      session.jsonl                    # pi writes here directly (--session flag)
+  ready/                               # completion markers for hook notification
+    <job-id>                           # empty file, existence = "done"
+```
+
+### status.json (overwritten per lifecycle event)
+
+```json
+{
+  "id": "a1b2c3",
+  "specialist": "overthinker",
+  "status": "running",
+  "current_event": "tool_execution",
+  "current_tool": "bash(grep -r 'pattern' src/)",
+  "model": "anthropic/claude-sonnet-4-6",
+  "backend": "anthropic",
+  "pid": 48210,
+  "started_at_ms": 1710000000000,
+  "elapsed_s": 47,
+  "last_event_at_ms": 1710000047000,
+  "bead_id": "bead-xyz",
+  "session_file": ".specialists/jobs/a1b2c3/session.jsonl",
+  "error": null
+}
+```
+
+On completion, status changes to "done" and elapsed_s is final.
+On error, status is "error" and error field contains the message.
+On cancel, status is "cancelled".
+On stall detection, status remains "running" but a "stalled": true field is added.
+
+### events.jsonl (append-only, lifecycle + tool events)
+
+```jsonl
+{"ts":1710000000,"event":"starting","specialist":"overthinker","model":"anthropic/claude-sonnet-4-6","id":"a1b2c3"}
+{"ts":1710000003,"event":"thinking"}
+{"ts":1710000008,"event":"toolcall","tool":"read","args":"src/index.ts"}
+{"ts":1710000009,"event":"tool_execution","tool":"read"}
+{"ts":1710000009,"event":"tool_execution_end","tool":"read","duration_ms":340}
+{"ts":1710000015,"event":"toolcall","tool":"bash","args":"grep -r 'pattern' src/"}
+{"ts":1710000016,"event":"tool_execution","tool":"bash"}
+{"ts":1710000022,"event":"tool_execution_end","tool":"bash","duration_ms":6100}
+{"ts":1710000030,"event":"text"}
+{"ts":1710000047,"event":"done","duration_ms":47000,"session_file":".specialists/jobs/a1b2c3/session.jsonl"}
+```
+
+NOT captured in events.jsonl: thinking_delta content, text_delta content, message_start,
+thinking_end. These are high-frequency events that add noise without diagnostic value.
+
+### result.txt
+
+Plain text. The clean final assistant output extracted from pi's get_last_assistant_text
+RPC call. Written once on agent_end. This is what `specialists result <id>` prints.
+
+### session.jsonl
+
+Pi's native session file. Written by pi directly via `--session <path>`. Contains the full
+message history (user, assistant, tool calls, tool results) in pi's internal JSONL format.
+Used for `--continue` multi-turn resumption. We never read or parse this file — pi owns it.
+
+---
+
+## 3. CLI Commands
+
+### 3.1 specialists run <name> (MODIFIED — add --background)
+
+```
+specialists run <name> --prompt "..." [--background] [--model <model>] [--no-beads]
+                       [--continue <job-id>] [--timeout <ms>]
+```
+
+**Foreground (default, existing behavior)**: Streams pi output to stdout in real time.
+Blocks until completion. Exit code reflects success/failure.
+
+**Background (--background, new)**: Spawns pi subprocess, prints job ID to stdout, writes
+status/events/result files. The `specialists run` process stays alive as a supervisor
+(not a daemon) — Claude backgrounds it with `&` in bash.
+
+**Continue (--continue <job-id>)**: Reads session file path from
+`.specialists/jobs/<job-id>/session.txt` or from status.json. Spawns pi with
+`--session <path>`. Full context from previous run is available.
+
+Supervisor lifecycle (--background mode):
+1. Generate job ID (nanoid or uuid short)
+2. Create .specialists/jobs/<id>/ directory
+3. Write initial status.json (status: "starting")
+4. Run pre-scripts (existing mechanism, unchanged)
+5. Spawn pi subprocess with --mode rpc, --session .specialists/jobs/<id>/session.jsonl
+6. Print job ID to stdout: "Job started: <id>"
+7. Read NDJSON from pi stdout:
+   - On lifecycle/tool events → update status.json, append to events.jsonl
+   - On thinking_start/text_delta → update current_event in status.json only (no content)
+   - Track last_event_at_ms for stall detection
+8. On agent_end:
+   a. Send {"type": "get_last_assistant_text"} via stdin → read response → write result.txt
+   b. Update status.json to "done"
+   c. Write done event to events.jsonl
+   d. Touch .specialists/ready/<id> (for hook notification)
+   e. Close stdin → pi exits
+9. Run post-scripts (existing mechanism, unchanged)
+10. Close beads issue (if created)
+11. Supervisor process exits
+
+Stall detection (in-process, not a daemon):
+- Configurable per-specialist via stall_timeout_ms in YAML (default: null = disabled)
+- If last_event_at_ms is older than stall_timeout_ms, write "stalled": true to status.json
+- Do NOT auto-kill — surface the stall in status, let Claude or the user decide
+
+Error handling:
+- Pi process exits non-zero without agent_end → write status "error", close bead as ERROR
+- Pi process killed by OOM/signal → same as above, capture exit code in error field
+- Pre-script failure → write to status.json, still start pi (pre-script output is context, not a gate)
+- Post-script failure → swallow silently (existing behavior, unchanged)
+
+### 3.2 specialists status (MODIFIED — add job status)
+
+```
+specialists status [--job <id>] [--json]
+```
+
+Without --job: existing system health output (specialist count, pi version, beads status,
+MCP registration) PLUS a job summary table:
+
+```
+── Active Jobs ───────────────────────────────────────────────────────────
+  a1b2c3  overthinker   running  1m12s  tool: bash(grep -r ...)
+  d4e5f6  bug-hunt      running  0m34s  thinking
+  g7h8i9  init-session  done     0m08s  ✓
+```
+
+With --job <id>: detailed single-job view:
+
+```
+  overthinker | running | 1m12s | model: anthropic/claude-sonnet-4-6
+  Current: tool_execution bash(grep -r 'pattern' src/)
+  Bead: bead-xyz
+  Session: .specialists/jobs/a1b2c3/session.jsonl
+  Events: 14 (5 tool calls)
+```
+
+Implementation: reads .specialists/jobs/*/status.json. Pure file reads, no MCP, no
+subprocess interaction.
+
+### 3.3 specialists result <id> (NEW)
+
+```
+specialists result <id> [--raw]
+```
+
+Prints result.txt to stdout. If the job is still running, prints current status and exits
+with code 1. --raw skips any formatting/headers and prints only the raw result text.
+
+### 3.4 specialists feed (NEW)
+
+```
+specialists feed [--job <id>] [--follow]
+```
+
+Formatted tail of events.jsonl files. Without --job, shows all active jobs interleaved
+with job ID prefix. --follow keeps tailing (like tail -f).
+
+Output format:
+```
+[a1b2c3] overthinker  00:12  toolcall    bash(grep -r 'pattern' src/)
+[a1b2c3] overthinker  00:18  tool_end    bash  6.1s
+[d4e5f6] bug-hunt     00:34  thinking
+[a1b2c3] overthinker  00:22  text
+[a1b2c3] overthinker  00:47  done        47.0s
+```
+
+### 3.5 specialists stop <id> (NEW — CLI equivalent of MCP stop_specialist)
+
+```
+specialists stop <id>
+```
+
+Reads status.json for the PID, sends SIGTERM. If the supervisor process is still alive,
+it detects the child exit, writes "cancelled" status, closes bead. If the supervisor
+is gone (orphaned pi process), sends SIGTERM directly to the PID.
+
+### 3.6 specialists run (EXISTING — foreground, unchanged)
+
+Existing behavior preserved. No --background flag = streams to stdout, blocks until done.
+Used by humans directly and by Claude for quick synchronous tasks where background
+overhead is not worth it.
+
+---
+
+## 4. Pi Subprocess Protocol
+
+### 4.1 Spawn Arguments
+
+```
+pi --mode rpc \
+   --provider <provider> \
+   --model <model> \
+   --append-system-prompt <system_prompt> \
+   --tools <tool_list>                          # always set — see below
+   --skill <path>                               # repeated for each skills.paths entry
+   --session .specialists/jobs/<id>/session.jsonl \
+   --no-extensions                              # prevent user extensions from emitting UI requests
+   <any additional args from specialist config>
+```
+
+**--append-system-prompt**: The specialist's prompt.system field. Takes priority over
+AGENTS.md. This IS the specialist's identity — its behavioral constraints, output format
+requirements, and role definition. Not template-rendered (no variable substitution).
+
+**--no-extensions**: Always set in background mode. User-installed pi extensions can emit
+`extension_ui_request` events (dialogs, confirmations) on stdout and block waiting for a
+response from stdin. The supervisor never sends these responses — causing a silent hang.
+`--no-extensions` disables extension discovery entirely. (`--no-input` does not exist in pi.)
+
+**--tools**: Always set explicitly. Pi's default when no `--tools` flag is passed is
+`read,bash,edit,write` — which silently excludes `grep`, `find`, and `ls`. Per-tier mapping:
+
+| Permission | --tools value |
+|------------|---------------|
+| READ_ONLY  | `read,bash,grep,find,ls` |
+| BASH_ONLY  | `bash` |
+| LOW        | `read,bash,edit,write,grep,find,ls` |
+| MEDIUM     | `read,bash,edit,write,grep,find,ls` |
+| HIGH       | `read,bash,edit,write,grep,find,ls` |
+
+`mapPermissionToTools()` in `src/pi/session.ts` must be updated to match this table.
+
+**--skill**: One flag per entry in the specialist's skills.paths array. Paths resolved:
+- Absolute paths: passed as-is
+- ~/... paths: expanded to home directory
+- Relative paths: resolved from project root (cwd)
+- Missing paths: logged as warning in events.jsonl, not fatal
+
+**--session**: Always set in --background mode. Points to
+.specialists/jobs/<id>/session.jsonl. Pi creates and writes this file. We never read it
+directly — it's pi's internal format. We store the path for --continue.
+
+### 4.2 Stdin RPC Commands
+
+The supervisor sends three types of commands via stdin, all as JSON + newline:
+
+**Prompt** (on start):
+```json
+{"type": "prompt", "message": "<rendered task template>"}
+```
+
+> **Important**: Pi's RPC mode responds to `prompt` immediately with
+> `{"type":"response","command":"prompt","success":true}` — this is an ack that the command
+> was received, NOT a completion signal. The agent starts working asynchronously after this
+> ack. The supervisor must NOT treat the prompt response as completion — it must continue
+> reading stdout events until `agent_end` arrives.
+
+**Get state** (after agent_end, before close):
+```json
+{"type": "get_state"}
+```
+Response includes sessionFile, sessionId, isStreaming, model. We extract sessionFile
+to confirm the session path (should match what we passed via --session).
+
+**Get last assistant text** (after agent_end, before close):
+```json
+{"type": "get_last_assistant_text"}
+```
+Response: `{"type":"response","command":"get_last_assistant_text","success":true,"data":{"text":"..."|null}}`
+
+`data.text` is `null` if no assistant message exists (e.g. pi crashed before responding).
+The supervisor must null-check before writing result.txt — write an empty file or skip
+writing entirely if `text` is null.
+
+**Close**: stdin.end() — sends EOF, pi exits. Only called after the above two queries
+complete. This replaces the current stdin.end() hack that fires immediately after prompt.
+
+### 4.3 Stdout NDJSON Event Processing
+
+Events read from pi's stdout, one JSON object per line. The supervisor categorizes:
+
+**Status-updating events** (update status.json current_event + current_tool):
+- thinking_start, thinking_delta → current_event: "thinking"
+- toolcall_start → current_event: "toolcall", current_tool: tool name + args
+- tool_execution_start, tool_execution_update → current_event: "tool_execution"
+- tool_execution_end → current_event: "tool_execution_end"
+- message_update with text_delta → current_event: "text"
+- agent_end → triggers finalization sequence (4.2 above)
+
+**JSONL-logged events** (append to events.jsonl):
+- thinking_start (not deltas — just the transition)
+- toolcall_start (with tool name and args summary)
+- tool_execution_end (with tool name and duration)
+- text (first text_delta only — marks transition to output)
+- agent_end (with duration)
+
+**Dropped events** (not written anywhere):
+- thinking_delta (high frequency, content not needed)
+- thinking_end (redundant — next event implies it)
+- text_delta content (high frequency, full text available via get_last_assistant_text)
+- message_start (metadata only, captured elsewhere)
+
+### 4.4 No stdin.end() on prompt
+
+This is the key protocol change from current PiAgentSession. Currently, prompt() calls
+stdin.end() immediately to trigger EOF, which makes every session single-turn. In v3:
+
+1. prompt() sends the JSON command via stdin.write(), does NOT close stdin
+2. Supervisor reads NDJSON events from stdout until agent_end
+3. Supervisor sends get_state and get_last_assistant_text queries via stdin
+4. Supervisor calls stdin.end() only after receiving both responses
+5. Pi sees EOF, exits cleanly
+
+This enables multi-turn (--continue) because the session file is complete and valid.
+Pi wrote the full conversation to the session JSONL during execution.
+
+---
+
+## 5. Schema Changes (.specialist.yaml)
+
+### 5.1 New field: skills.paths
+
+```yaml
+skills:
+  paths:                                    # NEW — pi --skill injection
+    - ~/.agents/skills/docker-patterns/     # user-scope skill directory
+    - ./skills/mercury-infra/               # project-scope skill directory
+  scripts:                                  # EXISTING — unchanged
+    - path: ./scripts/check-env.sh
+      phase: pre
+      inject_output: true
+```
+
+skills.paths is an optional array of strings. Each entry becomes a --skill <path> flag
+on the pi command line. Pi loads these as on-demand context (README files, tool
+definitions, etc.) that the model can reference without bloating the initial prompt.
+
+Path resolution:
+- ~/... → os.homedir() + rest
+- ./... → path.resolve(cwd, rest)
+- /... → absolute, as-is
+
+Validation: paths are validated at specialist load time (loader.ts). Missing paths
+produce a warning log, not a load failure. This allows user-scope skills that may not
+exist on every machine.
+
+### 5.2 New field: execution.stall_timeout_ms
+
+```yaml
+execution:
+  stall_timeout_ms: 30000                   # NEW — optional, default: null (disabled)
+```
+
+If set, the supervisor checks last_event_at_ms on a 5-second interval. If no event
+received for stall_timeout_ms, writes "stalled": true to status.json. Does NOT auto-kill.
+Surfaces in `specialists status` output.
+
+### 5.3 Existing fields — no changes
+
+All existing schema fields remain unchanged:
+- metadata (name, version, description, category, tags, updated)
+- execution (mode, model, fallback_model, timeout_ms, response_format, permission_required)
+- prompt (system, task_template, skill_inherit)
+- skills.scripts (path, phase, inject_output)
+- communication (publishes)
+- beads_integration (auto, always, never)
+
+---
+
+## 6. Hook Notification
+
+### 6.1 Completion hook (NEW — UserPromptSubmit)
+
+File: ~/.claude/hooks/specialists-complete.mjs (installed by `specialists install`)
+
+Trigger: UserPromptSubmit — fires on every user message in Claude Code.
+
+Logic:
+1. Scan .specialists/ready/ for any files
+2. For each file found:
+   a. Read .specialists/jobs/<id>/status.json
+   b. Format one-line banner
+   c. Delete the ready marker file (prevents repeat notifications)
+3. Inject banner(s) into the prompt
+
+Banner format:
+```
+[Specialist 'overthinker' completed (job a1b2c3, 1m47s). Run: specialists result a1b2c3]
+```
+
+Multiple completions produce multiple banners, one per line.
+
+If no ready markers exist, hook exits silently (no injection, no overhead).
+
+### 6.2 Existing hooks — unchanged
+
+The four existing hooks (main-guard, beads-edit-gate, beads-commit-gate, beads-stop-gate)
+are unchanged. The new hook is additive.
+
+---
+
+## 7. PiAgentSession Changes
+
+### 7.1 Current interface (SessionFactory — 6 methods)
+
+```typescript
+start(): Promise<void>           // spawn subprocess
+prompt(task: string): Promise<void>  // send task, currently closes stdin
+waitForDone(): Promise<void>     // resolve on agent_end
+getLastOutput(): Promise<string> // return final text
+kill(): void                     // SIGTERM + cleanup
+meta: { backend, model, sessionId, startedAt }
+```
+
+### 7.2 Modified interface
+
+```typescript
+start(): Promise<void>           // spawn subprocess (unchanged)
+prompt(task: string): Promise<void>  // send RPC prompt command, DO NOT close stdin
+waitForDone(timeout?: number): Promise<void>  // resolve on agent_end, with timeout
+getLastOutput(): Promise<string> // send get_last_assistant_text RPC, return response
+getState(): Promise<SessionState>  // send get_state RPC, return session info
+close(): Promise<void>           // send EOF (stdin.end()), wait for process exit
+kill(): void                     // SIGTERM + cleanup (unchanged, for abort/cancel)
+meta: { backend, model, sessionId, startedAt }
+```
+
+Changes:
+1. prompt() sends {"type": "prompt", "message": task} via stdin.write(), no stdin.end()
+2. waitForDone() adds optional timeout parameter — Promise.race with timeout
+3. getLastOutput() sends {"type": "get_last_assistant_text"} via stdin, parses response
+4. getState() NEW — sends {"type": "get_state"} via stdin, parses response
+5. close() NEW — calls stdin.end(), waits for process exit event
+6. kill() unchanged — SIGTERM, idempotent
+
+The supervisor sequence becomes:
+```
+await session.start()
+await session.prompt(renderedTask)
+await session.waitForDone(timeoutMs)    // blocks until agent_end or timeout
+const output = await session.getLastOutput()  // RPC query
+const state = await session.getState()        // RPC query
+await session.close()                         // EOF → clean exit
+```
+
+### 7.3 NDJSON handling — unchanged
+
+The manual line buffer (_lineBuffer + split on \n + process complete lines) is correct
+and handles large payloads (100KB+ agent_end events). No change needed. The only
+difference: agent_end no longer triggers stdin.end(). It resolves the waitForDone()
+promise, and the supervisor decides when to query state and close.
+
+### 7.4 RPC response handling — new
+
+Currently, PiAgentSession only reads events from stdout. It never sends commands via
+stdin (except the implicit single prompt via the CLI args). With the new protocol:
+
+After agent_end, stdin is still open. The supervisor sends JSON commands and reads
+responses from stdout. Responses are JSON objects with type: "response", keyed by the
+command type. The existing NDJSON line reader handles these — they arrive as regular
+JSON lines on stdout.
+
+Parsing:
+```typescript
+// After agent_end, switch to command-response mode
+async sendCommand(cmd: object): Promise<any> {
+  const line = JSON.stringify(cmd) + '\n';
+  this.proc.stdin.write(line);
+  // Wait for next complete JSON line on stdout that is a response
+  return new Promise((resolve) => {
+    this._pendingCommand = resolve;
+  });
+}
+```
+
+The _handleLine method checks: if the parsed JSON has type === "response", resolve
+_pendingCommand. Otherwise, process as a normal event.
+
+---
+
+## 8. SpecialistRunner Changes
+
+### 8.1 Background mode support
+
+SpecialistRunner.run() currently blocks until completion. For --background, the CLI's
+run command handles the lifecycle — it calls runner.run() with callbacks that write to
+files instead of streaming to stdout.
+
+The runner itself does NOT need a "background mode". The CLI command is the supervisor.
+Runner provides the execution; the CLI provides the lifecycle management.
+
+### 8.2 Session path passthrough
+
+Runner must accept an optional sessionPath in PiSessionOptions and pass it through to
+PiAgentSession.start() as the --session flag. For --continue, the CLI reads the session
+path from the previous job's status.json and passes it to the runner.
+
+### 8.3 Skills paths passthrough
+
+Runner must accept an optional skillPaths: string[] in PiSessionOptions and pass each
+as a --skill flag. Skills paths come from the specialist's YAML config (skills.paths),
+resolved by the loader at discovery time.
+
+### 8.4 Timeout enforcement
+
+Runner should pass execution.timeout_ms to session.waitForDone(timeout). On timeout,
+call session.kill() and throw a TimeoutError. Circuit breaker records the failure.
+
+---
+
+## 9. MCP Server Changes
+
+### 9.1 Retained tools
+
+**specialist_init**: Unchanged. Returns available specialists and beads status.
+
+**list_specialists**: Unchanged. Pure read.
+
+**specialist_status**: Modified — add job summary from .specialists/jobs/*/status.json.
+Returns circuit breaker health + active/recent job list.
+
+**use_specialist**: Unchanged. Synchronous execution for quick tasks. Calls runner.run()
+directly. Appropriate for sub-15-second specialists (init-session, report-generator).
+
+### 9.2 Deprecated tools
+
+**start_specialist**: Deprecated. Replaced by `specialists run --background` via bash.
+Keep functional for backward compatibility but add a note in the tool description
+suggesting the CLI alternative.
+
+**poll_specialist**: Deprecated. Replaced by `specialists status` and
+`specialists result` via bash.
+
+**stop_specialist**: Deprecated. Replaced by `specialists stop` via bash.
+
+**run_parallel**: Deprecated. Claude can run multiple `specialists run --background &`
+commands. Or use the synchronous path for quick parallel tasks via use_specialist.
+
+### 9.3 SIGTERM handler (NEW)
+
+```typescript
+process.on('SIGTERM', () => {
+  // Kill all running pi subprocesses managed by use_specialist (sync path)
+  registry.getAllRunning().forEach(job => job.killFn?.());
+  process.exit(0);
+});
+```
+
+Only covers the MCP server's own subprocess (use_specialist sync path). Background
+jobs are owned by their supervisor processes, not the MCP server.
+
+---
+
+## 10. Operational Concerns
+
+### 10.1 .gitignore
+
+`specialists init` must add `.specialists/` to .gitignore. Job files can contain full
+specialist output, session history, and environment variables from pre-scripts.
+
+### 10.2 Cleanup / GC
+
+On `specialists run --background` start, before creating the new job directory:
+scan .specialists/jobs/ and delete any directory older than 7 days. Configurable
+via SPECIALISTS_JOB_TTL_DAYS env var. Simple fs.stat + rm -rf.
+
+### 10.3 Beads crash recovery
+
+On `specialists run --background` start (same GC scan): check for jobs with
+status "running" that have no live process (PID check). Close their beads as ERROR.
+Mark status as "error" with error: "MCP server or supervisor crashed".
+
+### 10.4 File atomicity
+
+status.json: written via write-to-temp + fs.rename. Updated frequently (every lifecycle
+event), must never be half-written.
+
+events.jsonl: written via fs.appendFile with O_APPEND. Atomic for writes < 4KB on Linux.
+Event lines are well under 4KB.
+
+result.txt: written once via write-to-temp + fs.rename. Single write on completion.
+
+### 10.5 File descriptor management
+
+The supervisor opens events.jsonl for append at job start and keeps the fd open for the
+duration. On completion, error, or cancel: fd.close() is called in a finally block.
+On supervisor crash: OS closes the fd automatically.
+
+---
+
+## 11. Migration Path
+
+### Phase 1: File layout + background mode (HIGH VALUE, LOW RISK)
+
+1. Create .specialists/ directory structure
+2. Add --background flag to `specialists run`
+3. Implement supervisor lifecycle (status.json, events.jsonl, result.txt)
+4. Add `specialists status` job listing (reads status.json files)
+5. Add `specialists result` command
+6. Add `specialists feed` command
+7. Add `specialists stop` command (CLI)
+8. Add .gitignore entry in `specialists init`
+9. Add GC on startup
+
+Does NOT touch: PiAgentSession internals, MCP tools, SpecialistRunner.
+Uses existing PiAgentSession with its current limitations (single-turn only, no RPC
+queries post-completion). result.txt is populated from the existing getLastOutput()
+which reads from the in-memory _lastOutput captured at agent_end.
+
+This phase delivers: background execution, lightweight status polling via bash,
+full output retrieval, feed/debugging CLI. Everything except multi-turn and RPC queries.
+
+### Phase 2: PiAgentSession protocol upgrade (MEDIUM VALUE, MEDIUM RISK)
+
+1. Remove stdin.end() from prompt() — send RPC JSON command instead
+2. Add waitForDone(timeout) with Promise.race
+3. Add getState() RPC command
+4. Add getLastOutput() via RPC (replaces in-memory capture)
+5. Add close() method (explicit EOF)
+6. Add --session flag passthrough
+7. Add --skill flag passthrough
+8. Add stall detection (in-process setInterval in supervisor)
+9. Update SpecialistRunner for sessionPath and skillPaths options
+
+Prerequisite: verify that pi --mode rpc accepts JSON commands on stdin (not just
+CLI args). The audit's PiAgentSession code and pi's RPC docs both indicate this works,
+but test before implementing.
+
+This phase delivers: multi-turn via --continue, session persistence, skill injection,
+timeout enforcement, stall detection.
+
+### Phase 3: Hook notification + MCP deprecation (LOW VALUE, LOW RISK)
+
+1. Create specialists-complete.mjs hook
+2. Add to `specialists install` hook deployment
+3. Add deprecation notes to start_specialist, poll_specialist, stop_specialist,
+   run_parallel tool descriptions
+4. Add SIGTERM handler to MCP server
+
+### Phase 4: Schema + built-in specialist updates
+
+1. Add skills.paths to schema (zod validation, loader resolution)
+2. Add execution.stall_timeout_ms to schema
+3. Update built-in specialists to use skills.paths where appropriate
+4. Create example skill directories in ~/.agents/skills/
+
+---
+
+## 12. Testing Strategy
+
+### Phase 1 tests
+
+- Supervisor lifecycle: mock PiAgentSession, verify status.json written at each stage
+- status.json atomicity: concurrent write + read, verify no partial JSON
+- events.jsonl: verify correct events logged, no thinking deltas
+- result.txt: verify written only on completion, not on error/cancel
+- GC: create old job dirs, verify cleanup
+- specialists status: verify reads from file, formats correctly
+- specialists result: verify returns result.txt content, error if still running
+- specialists stop: verify SIGTERM sent to correct PID
+
+### Phase 2 tests
+
+- RPC prompt command: verify JSON sent via stdin, stdin NOT closed
+- RPC get_state: verify command sent after agent_end, response parsed
+- RPC get_last_assistant_text: verify command sent, response parsed
+- close(): verify stdin.end() called, process exit awaited
+- waitForDone(timeout): verify timeout triggers kill + rejection
+- Stall detection: verify stalled flag set after configurable interval
+- --session flag: verify passed to pi subprocess args
+- --skill flag: verify each skills.paths entry becomes a --skill arg
+- --continue: verify session path read from previous job, passed to pi
+
+### Phase 1 does NOT require
+
+- Integration tests against real pi subprocess (existing mock-based tests cover this)
+- MCP tool handler tests (tools are unchanged in Phase 1)
+- NDJSON parser tests (parser is unchanged in Phase 1)
+
+---
+
+## 13. Verification Checklist
+
+All items verified against pi-mono source (packages/coding-agent) and pi --help output.
+
+- [x] `pi --mode rpc` accepts {"type": "prompt", "message": "..."} on stdin
+      — confirmed: rpc-mode.ts handleCommand case "prompt"
+- [x] `pi --session /arbitrary/path/session.jsonl` accepts paths outside ~/.pi/
+      — confirmed: main.ts resolveSessionPath() treats any arg containing "/" as a direct path
+- [x] `pi --append-system-prompt "..."` exists and works as expected
+      — confirmed: pi --help
+- [x] `pi --skill <path>` loads skill directories correctly, repeatable
+      — confirmed: pi --help
+- [x] After agent_end, pi accepts further stdin commands before stdin is closed
+      — confirmed: runRpcMode() never exits on agent_end; loop runs until stdin EOF
+- [x] `get_state` response includes sessionFile field
+      — confirmed: rpc-mode.ts get_state handler: sessionFile: session.sessionFile
+- [x] `get_last_assistant_text` returns clean text
+      — confirmed: agent-session.ts getLastAssistantText(); returns null (not empty string)
+      when no assistant message exists — null-guard required before writing result.txt
+
+**Additional findings from pi-mono source audit:**
+
+- `--no-input` does not exist in pi — removed from spawn args (section 4.1)
+- `prompt` RPC command responds with an immediate ack, not a completion signal — supervisor
+  must keep reading stdout until agent_end (see section 4.2 note)
+- `--no-extensions` required to prevent user extensions from hanging the supervisor
+  via unanswered extension_ui_request events (see section 4.1)
+- Pi's `--tools` default (`read,bash,edit,write`) excludes grep/find/ls — all tiers now
+  use explicit tool lists in mapPermissionToTools() (see section 4.1 table)