docs: correct pi harness paths and the task tool's scope (#390)

The pi migration moved several files without updating CLAUDE.md:

- ai/pi-executor.ts -> ai/pi/pi-executor.ts
- ai/settings-writer.ts:writeCodePathPermissionConfig ->
  ai/pi/permission-system.ts:syncPermissionSystemConfig
- ai/tools.ts -> ai/pi/task-tool.ts and ai/pi/session-tools.ts
- src/mcp-server/ -> src/collectors/

Also correct the task tool's description: it was documented as
read-only, but CHILD_TOOLS grants read, grep, find, ls, write, and
bash. Drop the stale MCP label from the collectors and the SDK
reference in .env.example.

.env.example

@@ -18,7 +18,7 @@ ANTHROPIC_API_KEY=your-api-key-here
 # =============================================================================
 # OPTION 2: Custom Base URL (compatible proxies, gateways, etc.)
 # =============================================================================
-# Point the SDK at an alternative Anthropic-compatible endpoint.
+# Point the agent at an alternative Anthropic-compatible endpoint.
 # ANTHROPIC_BASE_URL=https://your-proxy.example.com
 # ANTHROPIC_AUTH_TOKEN=your-auth-token   # Auth token for the custom endpoint
 

CLAUDE.md

@@ -127,7 +127,7 @@ Infra (Temporal) runs via `docker-compose.yml`. Workers are ephemeral `docker ru
 - `apps/worker/src/paths.ts` — Centralized path constants (`PROMPTS_DIR`, `CONFIGS_DIR`, `WORKSPACES_DIR`)
 - `apps/worker/src/session-manager.ts` — Agent definitions (`AGENTS` record). Agent types in `apps/worker/src/types/agents.ts`
 - `apps/worker/src/config-parser.ts` — YAML config parsing with JSON Schema validation
-- `apps/worker/src/ai/pi-executor.ts` — pi harness integration (retry disabled; Temporal owns retry)
+- `apps/worker/src/ai/pi/pi-executor.ts` — pi harness integration (retry disabled; Temporal owns retry)
 - `apps/worker/src/services/` — Business logic layer (Temporal-agnostic). Activities delegate here. Key: `agent-execution.ts`, `error-handling.ts`, `container.ts`
 - `apps/worker/src/types/` — Consolidated types: `Result<T,E>`, `ErrorCode`, `AgentName`, `ActivityLogger`, etc.
 - `apps/worker/src/utils/` — Shared utilities (file I/O, formatting, concurrency)
@@ -150,9 +150,9 @@ Durable workflow orchestration with crash recovery, queryable progress, intellig
 5. **Reporting** (`report`) — Executive-level security report
 
 ### Supporting Systems
-- **Configuration** — YAML configs in `apps/worker/configs/` with JSON Schema validation (`config-schema.json`). Supports auth settings (MFA/TOTP), URL/code rule scoping (`rules.avoid`/`rules.focus`), run-scope steering (`vuln_classes`, `exploit`), free-form `rules_of_engagement`, and post-hoc `report` filters (`min_severity`, `min_confidence`, `guidance`). `code_path` avoid rules are enforced via the `@gotgenes/pi-permission-system` extension: `apps/worker/src/temporal/activities.ts:syncCodePathDenyRules` writes a global `path` deny config once per workflow (`apps/worker/src/ai/settings-writer.ts:writeCodePathPermissionConfig`), and the executor loads the extension when that config is present (`apps/worker/src/ai/pi-executor.ts`), so denies fire across every tool and child `task` session. `vuln_classes`/`exploit` scope is locked into `session.json` on first run; resumes with a different scope fail fast (`persistOrValidateRunScope`). Credential resolution — local mode: env vars → `./.env`; npx mode: env vars → `~/.shannon/config.toml` (via `npx @keygraph/shannon setup`)
+- **Configuration** — YAML configs in `apps/worker/configs/` with JSON Schema validation (`config-schema.json`). Supports auth settings (MFA/TOTP), URL/code rule scoping (`rules.avoid`/`rules.focus`), run-scope steering (`vuln_classes`, `exploit`), free-form `rules_of_engagement`, and post-hoc `report` filters (`min_severity`, `min_confidence`, `guidance`). `code_path` avoid rules are enforced via the `@gotgenes/pi-permission-system` extension: `apps/worker/src/temporal/activities.ts:syncCodePathDenyRules` writes a global `path` deny config once per workflow (`apps/worker/src/ai/pi/permission-system.ts:syncPermissionSystemConfig`), and the executor loads the extension when that config is present (`apps/worker/src/ai/pi/pi-executor.ts`), so denies fire across every tool and child `task` session. `vuln_classes`/`exploit` scope is locked into `session.json` on first run; resumes with a different scope fail fast (`persistOrValidateRunScope`). Credential resolution — local mode: env vars → `./.env`; npx mode: env vars → `~/.shannon/config.toml` (via `npx @keygraph/shannon setup`)
 - **Prompts** — Per-phase templates in `apps/worker/prompts/` with variable substitution (`{{TARGET_URL}}`, `{{CONFIG_CONTEXT}}`). Shared partials in `apps/worker/prompts/shared/` via `apps/worker/src/services/prompt-manager.ts`, including `_code-path-rules.txt` (focus/avoid `[FILE]`/`[GLOB]` routing) and `_rules-of-engagement.txt` (free-text engagement rules). When `exploit: false`, `apps/worker/src/services/findings-renderer.ts` deterministically converts each `*_exploitation_queue.json` into a `*_findings.md` for report assembly — no LLM in the loop
-- **Agent Harness (pi)** — Uses the **pi harness** (`@earendil-works/pi-coding-agent`, requires Node ≥ 22.19) via `apps/worker/src/ai/pi-executor.ts` (`runPiPrompt` → `createAgentSession`, retry disabled so Temporal owns retry). Models resolve through pi-ai in `apps/worker/src/ai/models.ts` (Anthropic / Bedrock / custom base URL via `ModelRegistry`+`AuthStorage`). pi ships no JSON-schema output or `Task`/`TodoWrite` built-ins, so structured queues are captured via a `submit_exploitation_queue` custom tool (`apps/worker/src/ai/queue-schemas.ts`), and `task` (read-only child sessions) + `todo_write` are provided as custom tools (`apps/worker/src/ai/tools.ts`); the per-phase MCP collectors are pi custom tools (TypeBox `defineTool` in `apps/worker/src/mcp-server/`). Adaptive thinking (pi's `medium` level) is enabled only on Opus 4.6/4.7/4.8 (`supportsAdaptiveThinking`); every other model runs with thinking `off`. Disable per-scan via `CLAUDE_ADAPTIVE_THINKING=false` (→ `off`) / `core.adaptive_thinking = false` (npx TOML). Browser automation via `playwright-cli` with session isolation (`-s=<session>`). TOTP generation via `generate-totp` CLI tool. Login flow template at `apps/worker/prompts/shared/login-instructions.txt` supports form, SSO, API, and basic auth. On authenticated whitebox scans, the `validate-authentication` preflight performs the single real login and saves the browser session to `auth-state.json` in the per-session audit directory (path from `authStateFile()` in `apps/worker/src/audit/utils.ts`, derived from `generateAuditPath()`). The validation activity (`apps/worker/src/services/validate-authentication.ts`) removes any stale file from a prior run before the agent runs and verifies the file parses and contains cookies or storage before the preflight is marked complete; `logWorkflowComplete` deletes it when the workflow ends so authenticated cookies don't sit on disk between scans. Agent prompts opt in to session reuse by `@include(shared/_shared-session.txt)` before their `<login_instructions>` block — the partial restores the session and falls through to the full login flow if verification fails. `vuln-auth`/`exploit-auth` omit the include and own their own login
+- **Agent Harness (pi)** — Uses the **pi harness** (`@earendil-works/pi-coding-agent`, requires Node ≥ 22.19) via `apps/worker/src/ai/pi/pi-executor.ts` (`runPiPrompt` → `createAgentSession`, retry disabled so Temporal owns retry). Models resolve through pi-ai in `apps/worker/src/ai/models.ts` (Anthropic / Bedrock / custom base URL via `ModelRegistry`+`AuthStorage`). pi ships no JSON-schema output or `Task`/`TodoWrite` built-ins, so structured queues are captured via a `submit_exploitation_queue` custom tool (`apps/worker/src/ai/queue-schemas.ts`), and `task` (child sessions scoped to `read`, `grep`, `find`, `ls`, `write`, and `bash` — no nested `task` or collector tools; `CHILD_TOOLS` in `apps/worker/src/ai/pi/task-tool.ts`) + `todo_write` (`apps/worker/src/ai/pi/session-tools.ts`) are provided as custom tools; the per-phase collectors are pi custom tools (TypeBox `defineTool` in `apps/worker/src/collectors/`). Adaptive thinking (pi's `medium` level) is enabled only on Opus 4.6/4.7/4.8 (`supportsAdaptiveThinking`); every other model runs with thinking `off`. Disable per-scan via `CLAUDE_ADAPTIVE_THINKING=false` (→ `off`) / `core.adaptive_thinking = false` (npx TOML). Browser automation via `playwright-cli` with session isolation (`-s=<session>`). TOTP generation via `generate-totp` CLI tool. Login flow template at `apps/worker/prompts/shared/login-instructions.txt` supports form, SSO, API, and basic auth. On authenticated whitebox scans, the `validate-authentication` preflight performs the single real login and saves the browser session to `auth-state.json` in the per-session audit directory (path from `authStateFile()` in `apps/worker/src/audit/utils.ts`, derived from `generateAuditPath()`). The validation activity (`apps/worker/src/services/validate-authentication.ts`) removes any stale file from a prior run before the agent runs and verifies the file parses and contains cookies or storage before the preflight is marked complete; `logWorkflowComplete` deletes it when the workflow ends so authenticated cookies don't sit on disk between scans. Agent prompts opt in to session reuse by `@include(shared/_shared-session.txt)` before their `<login_instructions>` block — the partial restores the session and falls through to the full login flow if verification fails. `vuln-auth`/`exploit-auth` omit the include and own their own login
 - **Audit System** — Crash-safe append-only logging in `workspaces/{hostname}_{sessionId}/`. The run directory's top level holds only the human-facing report (`Security-Assessment-Report.md`, `FINAL_REPORT_FILENAME` in `apps/worker/src/paths.ts`); everything else — deliverables, per-agent logs, prompts, `session.json`, `workflow.log`, and browser artifacts — is nested under a hidden `.shannon/` internals dir (`INTERNAL_DIR`) so a customer sees only the report. Audit path helpers route through `generateInternalPath` (`apps/worker/src/audit/utils.ts`); the CLI nests the overlay backing dirs under the same `.shannon/` (`apps/cli/src/docker.ts`, `start.ts`). `session.json`/`workflow.log` reads use dual-read resolvers (`resolveSessionJsonPath`, `resolveRunFile`) that prefer `.shannon/` and fall back to the legacy run-root layout, so pre-restructure workspaces stay listable (`workspaces`/`logs`) without migration. Resuming a pre-restructure workspace upgrades it in place first: `migrateLegacyWorkspaceLayout` (`apps/cli/src/commands/start.ts`) renames the flat deliverables/logs/session entries into `.shannon/` (carrying the deliverables `.git` along) before the overlay dirs are mounted, so resume finds the old checkpoints instead of re-running every agent. The report is surfaced by copying the assembled `comprehensive_security_assessment_report.md` from the deliverables dir to the run root (`copyReportToRunRoot` in `apps/worker/src/services/reporting.ts`). WorkflowLogger (`apps/worker/src/audit/workflow-logger.ts`) provides unified human-readable per-workflow logs, backed by LogStream (`apps/worker/src/audit/log-stream.ts`) shared stream primitive
 - **Deliverables** — Saved to `.shannon/deliverables/` in the target repo via the `save-deliverable` CLI script (`apps/worker/src/scripts/save-deliverable.ts`)
 - **Workspaces & Resume** — Named workspaces via `-w <name>` or auto-named from URL+timestamp. Resume detects completed agents via `session.json`. `loadResumeState()` in `apps/worker/src/temporal/activities.ts` validates deliverable existence, restores git checkpoints, and cleans up incomplete deliverables. Workspace listing via `apps/worker/src/temporal/workspaces.ts`
@@ -233,7 +233,7 @@ Comments must be **timeless** — no references to this conversation, refactorin
 
 **Entry Points:** `apps/worker/src/temporal/workflows.ts`, `apps/worker/src/temporal/activities.ts`, `apps/worker/src/temporal/worker.ts`
 
-**Core Logic:** `apps/worker/src/session-manager.ts`, `apps/worker/src/ai/pi-executor.ts`, `apps/worker/src/ai/settings-writer.ts` (writes `code_path` deny rules to the `@gotgenes/pi-permission-system` global config), `apps/worker/src/config-parser.ts`, `apps/worker/src/services/` (incl. `preflight.ts`, `findings-renderer.ts`, `reporting.ts`), `apps/worker/src/audit/`
+**Core Logic:** `apps/worker/src/session-manager.ts`, `apps/worker/src/ai/pi/pi-executor.ts`, `apps/worker/src/ai/pi/permission-system.ts` (writes `code_path` deny rules to the `@gotgenes/pi-permission-system` global config), `apps/worker/src/config-parser.ts`, `apps/worker/src/services/` (incl. `preflight.ts`, `findings-renderer.ts`, `reporting.ts`), `apps/worker/src/audit/`
 
 **Config:** `docker-compose.yml`, `apps/cli/infra/compose.yml`, `apps/worker/configs/`, `apps/worker/prompts/`, `tsconfig.base.json` (shared compiler options), `turbo.json`, `biome.json`