docs: note that v1 runs on the Claude Agent SDK and supports OAuth tokens

* feat: surface report at run root and nest run internals under .shannon

* feat: use plain-language wording in user-facing terminal messages

* feat(cli): guide users to watch scan progress and surface report path on start

* docs: sync run-folder layout and CLI wording across docs and comments

* feat(cli): add version command reporting package version or git SHA

* feat(cli): detect TTY for interactive prompts, color, and progress output

* docs: document --yes flag, version command, and tty module

* fix(cli): FORCE_COLOR precedence and plain uninstall --yes output

* fix(cli): respect empty NO_COLOR

* fix(cli): let NO_COLOR take precedence over FORCE_COLOR

* docs: mark claude-code-router integration as removed

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -69,9 +69,9 @@ body:
 
         Issues without this information may be difficult to triage.
 
-        - Check the workflow log:
-            - **npx mode:** `~/.shannon/workspaces/<workspace>/workflow.log`
-            - **Local mode:** `./workspaces/<workspace>/workflow.log`
+        - Check the scan log:
+            - **npx mode:** `~/.shannon/workspaces/<workspace>/.shannon/workflow.log`
+            - **Local mode:** `./workspaces/<workspace>/.shannon/workflow.log`
           Use `grep` or search to identify errors.
           Paste the relevant error output below.
         - Temporal:

CLAUDE.md

@@ -61,17 +61,20 @@ npx @keygraph/shannon setup
 ./shannon workspaces                                 # List all workspaces
 
 # Monitor
-./shannon logs <workspace>            # Tail workflow log
-./shannon status                      # Show running workers
-# Temporal Web UI: http://localhost:8233
+./shannon logs <workspace>            # Show a scan's live log
+./shannon status                      # Show running scans
+# Dashboard: http://localhost:8233
 
 # Stop
-./shannon stop                        # Preserves workflow data
-./shannon stop --clean                # Full cleanup including volumes (confirms first)
+./shannon stop                        # Preserves scan data
+./shannon stop --clean                # Full cleanup including volumes (confirms first; --yes/-y to skip)
+
+# Version
+./shannon version                     # npx: package version; local: git SHA
 
 # Image management
 ./shannon build [--no-cache]          # Local mode: build worker image
-npx @keygraph/shannon uninstall             # npx mode: remove ~/.shannon/ (confirms first)
+npx @keygraph/shannon uninstall             # npx mode: remove ~/.shannon/ (confirms first; --yes/-y to skip)
 
 # Build TypeScript (development)
 pnpm run build                       # Build all packages via Turborepo
@@ -82,7 +85,7 @@ pnpm biome:fix                       # Auto-fix lint, format, and import sorting
 
 **Monorepo tooling:** pnpm workspaces, Turborepo for task orchestration, Biome for linting/formatting. TypeScript compiler options shared via `tsconfig.base.json` at the root. All packages extend it, overriding only `rootDir` and `outDir`. Shared devDependencies (`typescript`, `@types/node`, `turbo`, `@biomejs/biome`) are hoisted to the root workspace.
 
-**Options:** `-c <file>` (YAML config), `-o <path>` (output directory), `-w <name>` (named workspace; auto-resumes if exists), `--pipeline-testing` (minimal prompts, 10s retries), `--debug` (preserve worker container after exit for log inspection)
+**Options:** `-c <file>` (YAML config), `-o <path>` (output directory), `-w <name>` (named workspace; auto-resumes if exists), `--pipeline-testing` (minimal prompts, 10s retries), `--debug` (preserve worker container after exit for log inspection), `--yes`/`-y` (skip the confirmation prompt on `stop --clean`/`uninstall`; required for non-interactive use)
 
 ## Architecture
 
@@ -96,7 +99,7 @@ apps/worker/     — @shannon/worker (private, Temporal worker + pipeline logic)
 ### CLI Package (`apps/cli/`)
 Published as `@keygraph/shannon` on npm. Contains only Docker orchestration logic — no Temporal SDK, business logic, or prompts. Bundled with tsdown for single-file ESM output.
 
-- `apps/cli/src/index.ts` — CLI dispatcher (`setup`, `start`, `stop`, `logs`, `workspaces`, `status`, `build`, `uninstall`, `info`)
+- `apps/cli/src/index.ts` — CLI dispatcher (`setup`, `start`, `stop`, `logs`, `workspaces`, `status`, `build`, `uninstall`, `version`)
 - `apps/cli/src/mode.ts` — Auto-detection: local mode if `SHANNON_LOCAL=1` env var is set
 - `apps/cli/src/docker.ts` — Compose lifecycle, image pull/build, ephemeral `docker run` worker spawning
 - `apps/cli/src/home.ts` — State directory management (`~/.shannon/` for npx, `./` for local)
@@ -105,6 +108,8 @@ Published as `@keygraph/shannon` on npm. Contains only Docker orchestration logi
 - `apps/cli/src/config/writer.ts` — TOML serialization and secure file persistence (0o600)
 - `apps/cli/src/commands/setup.ts` — Interactive TUI wizard (`@clack/prompts`) for provider credential setup (npx only)
 - `apps/cli/src/paths.ts` — Repo/config path resolution (bare name → `./repos/<name>`, or any absolute/relative path)
+- `apps/cli/src/version.ts` — Version reporting (npx: `package.json` version; local: `git-<sha>`)
+- `apps/cli/src/tty.ts` — Terminal capability detection: `requireInteractive` guard (fails fast off-TTY instead of hanging on a prompt), `supportsColor` color gating (`NO_COLOR`/`FORCE_COLOR`), and `stdoutIsTerminal` for spinner/cursor output
 - `apps/cli/src/commands/` — Command handlers
 - `apps/cli/infra/compose.yml` — Bundled Temporal compose file for npx mode
 - `apps/cli/tsdown.config.ts` — tsdown bundler config
@@ -148,8 +153,8 @@ Durable workflow orchestration with crash recovery, queryable progress, intellig
 - **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 written into `~/.claude/settings.json` `permissions.deny` (`Read`/`Edit`) once per workflow by `apps/worker/src/temporal/activities.ts:syncCodePathDenyRules` so the SDK enforces them at the tool layer even in `bypassPermissions` mode. `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
 - **SDK Integration** — Uses `@anthropic-ai/claude-agent-sdk` with `maxTurns: 10_000` and `bypassPermissions` mode. Adaptive thinking is enabled by default on Opus 4.6/4.7/4.8 (`supportsAdaptiveThinking` in `apps/worker/src/ai/models.ts`); disable per-scan via `CLAUDE_ADAPTIVE_THINKING=false` (env) or `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}/`. Tracks session metrics, per-agent logs, prompts, and deliverables. 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 `deliverables/` in the target repo via the `save-deliverable` CLI script (`apps/worker/src/scripts/save-deliverable.ts`)
+- **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`
 
 ## Development Notes

README.md

@@ -1,5 +1,7 @@
 > [!NOTE]
-> **[Shannon Now Runs on the Pi Harness (Beta) - run it today with `npx @keygraph/shannon@beta`](https://github.com/KeygraphHQ/shannon/discussions/358)**
+> **Shannon v1 (`v1.9.0`) runs on the Claude Agent SDK**, the last release before the pi harness. Running on the Claude Agent SDK means it can authenticate with an OAuth token from your Claude Code subscription instead of an Anthropic API key. Generate one with `claude setup-token`, then pick **OAuth Token** in `npx @keygraph/shannon@1.9.0 setup` or export it as `CLAUDE_CODE_OAUTH_TOKEN`.
+>
+> Shannon v2 replaced the Claude Agent SDK with the pi harness. See [Shannon 2.0 now runs on the Pi harness](https://github.com/KeygraphHQ/shannon/discussions/393).
 
 <div align="center">
 

apps/cli/src/commands/logs.ts

@@ -1,5 +1,5 @@
 /**
- * `shannon logs` command — tail a workspace's workflow log.
+ * `shannon logs` command — tail a scan's live log.
  *
  * Uses chokidar for reliable cross-platform file watching and
  * bounded synchronous reads to prevent duplicate output.
@@ -9,9 +9,10 @@ import fs from 'node:fs';
 import path from 'node:path';
 import { watch } from 'chokidar';
 import { getWorkspacesDir } from '../home.js';
+import { resolveRunFile } from '../paths.js';
 
 // Match the exact line the worker writes — anchored to prevent false positives from agent output
-const COMPLETION_PATTERN = /^Workflow (COMPLETED|FAILED)$/m;
+const COMPLETION_PATTERN = /^Scan (COMPLETED|FAILED)$/m;
 
 /** Read a byte range from a file and return it as a UTF-8 string. */
 function readRange(filePath: string, start: number, end: number): string {
@@ -31,30 +32,30 @@ function resolveLogFile(workspaceId: string): string {
   const workspacesDir = getWorkspacesDir();
 
   // 1. Direct match
-  const directPath = path.join(workspacesDir, workspaceId, 'workflow.log');
+  const directPath = resolveRunFile(path.join(workspacesDir, workspaceId), 'workflow.log');
   if (fs.existsSync(directPath)) return directPath;
 
   // 2. Resume workflow ID (e.g. workspace_resume_123)
   const resumeBase = workspaceId.replace(/_resume_\d+$/, '');
   if (resumeBase !== workspaceId) {
-    const resumePath = path.join(workspacesDir, resumeBase, 'workflow.log');
+    const resumePath = resolveRunFile(path.join(workspacesDir, resumeBase), 'workflow.log');
     if (fs.existsSync(resumePath)) return resumePath;
   }
 
   // 3. Named workspace ID (e.g. workspace_shannon-123)
   const namedBase = workspaceId.replace(/_shannon-\d+$/, '');
   if (namedBase !== workspaceId) {
-    const namedPath = path.join(workspacesDir, namedBase, 'workflow.log');
+    const namedPath = resolveRunFile(path.join(workspacesDir, namedBase), 'workflow.log');
     if (fs.existsSync(namedPath)) return namedPath;
   }
 
-  console.error(`ERROR: Workflow log not found for: ${workspaceId}`);
+  console.error(`ERROR: No scan found named: ${workspaceId}`);
   console.error('');
   console.error('Possible causes:');
-  console.error("  - Workflow hasn't started yet");
-  console.error('  - Workspace ID is incorrect');
+  console.error("  - The scan hasn't started yet");
+  console.error('  - The workspace name is incorrect');
   console.error('');
-  console.error('Check the Temporal Web UI at http://localhost:8233 for workflow details');
+  console.error('Check the dashboard at http://localhost:8233 for scan details');
   process.exit(1);
 }
 
@@ -82,7 +83,7 @@ export function logs(workspaceId: string): void {
     }
   }
 
-  console.log(`Tailing workflow log: ${logFile}`);
+  console.log(`Tailing scan log: ${logFile}`);
 
   // 1. Output existing content
   if (flush()) {

apps/cli/src/commands/setup.ts

@@ -10,12 +10,14 @@ import os from 'node:os';
 import path from 'node:path';
 import * as p from '@clack/prompts';
 import { type ShannonConfig, saveConfig } from '../config/writer.js';
+import { requireInteractive } from '../tty.js';
 
 const SHANNON_HOME = path.join(os.homedir(), '.shannon');
 
 type Provider = 'anthropic' | 'custom_base_url' | 'bedrock' | 'vertex';
 
 export async function setup(): Promise<void> {
+  requireInteractive('setup', 'For non-interactive use, export credentials as env vars (e.g. ANTHROPIC_API_KEY).');
   p.intro('Shannon Setup');
 
   // 1. Select provider

apps/cli/src/commands/start.ts

@@ -12,8 +12,9 @@ import { ensureImage, ensureInfra, randomSuffix, spawnWorker } from '../docker.j
 import { buildEnvFlags, loadEnv, validateCredentials } from '../env.js';
 import { getCredentialsPath, getWorkspacesDir, initHome } from '../home.js';
 import { isLocal } from '../mode.js';
-import { resolveConfig, resolveRepo } from '../paths.js';
+import { FINAL_REPORT_FILENAME, INTERNAL_DIR, resolveConfig, resolveRepo, resolveRunFile } from '../paths.js';
 import { displaySplash } from '../splash.js';
+import { stdoutIsTerminal } from '../tty.js';
 
 export interface StartArgs {
   url: string;
@@ -26,6 +27,29 @@ export interface StartArgs {
   version: string;
 }
 
+/**
+ * Upgrade a pre-restructure workspace (flat layout, no INTERNAL_DIR) before it is mounted,
+ * so resume finds the old deliverables and their git checkpoints instead of re-running every
+ * agent. For a legacy run every top-level entry is internal, so move them all into INTERNAL_DIR
+ * (a same-filesystem rename carries the deliverables .git along).
+ */
+function migrateLegacyWorkspaceLayout(workspacePath: string): void {
+  const legacySessionJson = path.join(workspacePath, 'session.json');
+  const internalPath = path.join(workspacePath, INTERNAL_DIR);
+  if (!fs.existsSync(legacySessionJson) || fs.existsSync(internalPath)) {
+    return;
+  }
+
+  fs.mkdirSync(internalPath, { recursive: true });
+  for (const entry of fs.readdirSync(workspacePath)) {
+    if (entry === INTERNAL_DIR) {
+      continue;
+    }
+    fs.renameSync(path.join(workspacePath, entry), path.join(internalPath, entry));
+  }
+  console.log(`Migrated workspace to ${INTERNAL_DIR}/ layout: ${workspacePath}`);
+}
+
 export async function start(args: StartArgs): Promise<void> {
   // 1. Initialize state directories and load env
   initHome();
@@ -61,12 +85,17 @@ export async function start(args: StartArgs): Promise<void> {
     args.workspace ?? `${new URL(args.url).hostname.replace(/[^a-zA-Z0-9-]/g, '-')}_shannon-${Date.now()}`;
 
   // 8. Create writable overlay directories (mounted over :ro repo paths inside container)
-  // Workspace dir must be 0o777 so the container user (UID 1001) can create audit subdirs
+  // The run dir and its INTERNAL_DIR must be 0o777 so the container user can create audit
+  // subdirs and the overlay backing dirs.
   const workspacePath = path.join(workspacesDir, workspace);
+  const internalPath = path.join(workspacePath, INTERNAL_DIR);
   fs.mkdirSync(workspacePath, { recursive: true });
   fs.chmodSync(workspacePath, 0o777);
+  migrateLegacyWorkspaceLayout(workspacePath);
+  fs.mkdirSync(internalPath, { recursive: true });
+  fs.chmodSync(internalPath, 0o777);
   for (const dir of ['deliverables', 'scratchpad', '.playwright-cli', '.playwright']) {
-    const dirPath = path.join(workspacePath, dir);
+    const dirPath = path.join(internalPath, dir);
     fs.mkdirSync(dirPath, { recursive: true });
     fs.chmodSync(dirPath, 0o777);
   }
@@ -119,7 +148,7 @@ export async function start(args: StartArgs): Promise<void> {
   const dockerExitCode = await new Promise<number>((resolve) => {
     proc.once('exit', (code) => resolve(code ?? 1));
     proc.once('error', (err) => {
-      console.error(`Failed to start worker: ${err.message}`);
+      console.error(`Failed to start the scan: ${err.message}`);
       resolve(1);
     });
   });
@@ -129,7 +158,7 @@ export async function start(args: StartArgs): Promise<void> {
   }
 
   // Detect whether this is a fresh workspace or a resume by checking session.json existence
-  const sessionJson = path.join(workspacesDir, workspace, 'session.json');
+  const sessionJson = resolveRunFile(path.join(workspacesDir, workspace), 'session.json');
   const isResume = fs.existsSync(sessionJson);
   let initialResumeCount = 0;
   if (isResume) {
@@ -141,8 +170,10 @@ export async function start(args: StartArgs): Promise<void> {
     }
   }
 
-  // Poll for workflow to register in session.json
-  process.stdout.write('Waiting for workflow to start...');
+  // Poll for workflow to register in session.json. Off-TTY, skip the dots and
+  // clear-line escape so redirected logs stay clean.
+  const animate = stdoutIsTerminal();
+  process.stdout.write('Waiting for the scan to start...');
   let workflowId = '';
   let started = false;
   let attempts = 0;
@@ -151,7 +182,7 @@ export async function start(args: StartArgs): Promise<void> {
     if (attempts > 60) {
       clearInterval(pollInterval);
       process.stdout.write('\n');
-      console.error('Timeout waiting for workflow to start');
+      console.error('Timed out waiting for the scan to start');
       process.exit(1);
     }
 
@@ -169,15 +200,15 @@ export async function start(args: StartArgs): Promise<void> {
         // Latest workflow ID: last resume attempt, or originalWorkflowId for fresh scans
         workflowId = resumeAttempts.at(-1)?.workflowId ?? session.session?.originalWorkflowId ?? '';
 
-        // Clear waiting line and show info
-        process.stdout.write('\r\x1b[K');
+        // Clear the waiting line, or just break it off-TTY
+        process.stdout.write(animate ? '\r\x1b[K' : '\n');
         printInfo(args, workspace, workflowId, repo.hostPath, workspacesDir);
         return;
       }
     } catch {
       // File doesn't exist yet
     }
-    process.stdout.write('.');
+    if (animate) process.stdout.write('.');
   }, 2000);
 
   // Stop the worker container only if it hasn't started yet
@@ -186,7 +217,7 @@ export async function start(args: StartArgs): Promise<void> {
     if (cleaned || started) return;
     cleaned = true;
     clearInterval(pollInterval);
-    console.log(`\nStopping worker ${containerName}...`);
+    console.log('\nStopping scan...');
     try {
       execFileSync('docker', ['stop', containerName], { stdio: 'pipe' });
     } catch {
@@ -224,8 +255,10 @@ function printInfo(
   workspacesDir: string,
 ): void {
   const logsCmd = isLocal() ? `./shannon logs ${workspace}` : `npx @keygraph/shannon logs ${workspace}`;
-  const reportsPath = path.join(workspacesDir, workspace);
+  const reportPath = path.join(workspacesDir, workspace, FINAL_REPORT_FILENAME);
 
+  console.log('  Scan started — it runs in the background, so you can close this terminal.');
+  console.log('');
   console.log(`  Target:     ${args.url}`);
   console.log(`  Repository: ${repoPath}`);
   console.log(`  Workspace:  ${workspace}`);
@@ -252,15 +285,15 @@ function printInfo(
   }
 
   console.log('');
-  console.log('  Monitor:');
+  console.log('  Watch scan progress:');
+  console.log(`    Live logs:  ${logsCmd}`);
   if (workflowId) {
-    console.log(`    Web UI:  http://localhost:8233/namespaces/default/workflows/${workflowId}`);
+    console.log(`    Dashboard:  http://localhost:8233/namespaces/default/workflows/${workflowId}`);
   } else {
-    console.log('    Web UI:  http://localhost:8233');
+    console.log('    Dashboard:  http://localhost:8233');
   }
-  console.log(`    Logs:    ${logsCmd}`);
   console.log('');
-  console.log('  Output:');
-  console.log(`    Reports: ${reportsPath}/`);
+  console.log('  Report (when the scan finishes):');
+  console.log(`    ${reportPath}`);
   console.log('');
 }

apps/cli/src/commands/status.ts

@@ -1,5 +1,5 @@
 /**
- * `shannon status` command — show running workers and Temporal health.
+ * `shannon status` command — show running scans and Temporal health.
  */
 
 import { isTemporalReady, listRunningWorkers } from '../docker.js';
@@ -9,16 +9,16 @@ export function status(): void {
   const temporalUp = isTemporalReady();
   console.log(`Temporal: ${temporalUp ? 'running' : 'not running'}`);
   if (temporalUp) {
-    console.log('  Web UI: http://localhost:8233');
+    console.log('  Dashboard: http://localhost:8233');
   }
   console.log('');
 
-  // 2. Running workers
+  // 2. Running scans
   const workers = listRunningWorkers();
   if (workers) {
-    console.log('Workers:');
+    console.log('Running scans:');
     console.log(workers);
   } else {
-    console.log('Workers: none running');
+    console.log('No scans running');
   }
 }

apps/cli/src/commands/stop.ts

@@ -4,9 +4,11 @@
 
 import * as p from '@clack/prompts';
 import { stopInfra, stopWorkers } from '../docker.js';
+import { requireInteractive } from '../tty.js';
 
-export async function stop(clean: boolean): Promise<void> {
-  if (clean) {
+export async function stop(clean: boolean, yes: boolean): Promise<void> {
+  if (clean && !yes) {
+    requireInteractive('stop --clean', 'Re-run with --yes to skip this confirmation.');
     const confirmed = await p.confirm({
       message: 'This will stop all running scans and remove the Temporal data. Continue?',
     });

apps/cli/src/commands/uninstall.ts

@@ -7,24 +7,34 @@ import os from 'node:os';
 import path from 'node:path';
 import * as p from '@clack/prompts';
 import { stopInfra, stopWorkers } from '../docker.js';
+import { requireInteractive } from '../tty.js';
 
 const SHANNON_HOME = path.join(os.homedir(), '.shannon');
 
-export async function uninstall(): Promise<void> {
-  p.intro('Shannon Uninstall');
+export async function uninstall(yes: boolean): Promise<void> {
+  const interactive = !yes;
+  if (interactive) p.intro('Shannon Uninstall');
 
   if (!fs.existsSync(SHANNON_HOME)) {
-    p.log.info('Nothing to remove. Shannon is not configured on this machine.');
-    p.outro('Done.');
+    const message = 'Nothing to remove. Shannon is not configured on this machine.';
+    if (interactive) {
+      p.log.info(message);
+      p.outro('Done.');
+    } else {
+      console.log(message);
+    }
     return;
   }
 
-  const confirmed = await p.confirm({
-    message: 'This will permanently remove all past scan data, saved configurations, and API keys. Continue?',
-  });
-  if (p.isCancel(confirmed) || !confirmed) {
-    p.cancel('Aborted.');
-    process.exit(0);
+  if (interactive) {
+    requireInteractive('uninstall', 'Re-run with --yes to skip this confirmation.');
+    const confirmed = await p.confirm({
+      message: 'This will permanently remove all past scan data, saved configurations, and API keys. Continue?',
+    });
+    if (p.isCancel(confirmed) || !confirmed) {
+      p.cancel('Aborted.');
+      process.exit(0);
+    }
   }
 
   // Stop any running containers first
@@ -32,6 +42,14 @@ export async function uninstall(): Promise<void> {
   stopInfra(false);
 
   fs.rmSync(SHANNON_HOME, { recursive: true, force: true });
-  p.log.success('All Shannon data has been removed.');
-  p.outro('Shannon has been uninstalled. Run `npx @keygraph/shannon setup` to start fresh.');
+
+  const done = 'All Shannon data has been removed.';
+  const hint = 'Shannon has been uninstalled. Run `npx @keygraph/shannon setup` to start fresh.';
+  if (interactive) {
+    p.log.success(done);
+    p.outro(hint);
+  } else {
+    console.log(done);
+    console.log(hint);
+  }
 }

apps/cli/src/config/resolver.ts

@@ -88,7 +88,9 @@ function loadTOML(): TOMLConfig | null {
     const mode = fs.statSync(configPath).mode;
     if (mode & 0o077) {
       const actual = (mode & 0o777).toString(8).padStart(3, '0');
-      console.error(`\nInsecure permissions (${actual}) on ${configPath}. Run: chmod 600 ${configPath}\n`);
+      console.error(
+        `\nYour config file is readable by other users on this machine (${actual}). Lock it down: chmod 600 ${configPath}\n`,
+      );
       process.exit(1);
     }
   }

apps/cli/src/docker.ts

@@ -13,6 +13,7 @@ import path from 'node:path';
 import { setTimeout as sleep } from 'node:timers/promises';
 import { fileURLToPath } from 'node:url';
 import { getMode } from './mode.js';
+import { INTERNAL_DIR } from './paths.js';
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 
@@ -116,7 +117,7 @@ export function ensureImage(version: string): void {
   if (exists) return;
 
   if (getMode() === 'local') {
-    console.log('Worker image not found, building...');
+    console.log('Shannon image not found, building...');
     buildImage(false);
   } else {
     console.log(`Pulling ${image}...`);
@@ -270,12 +271,13 @@ export function spawnWorker(opts: WorkerOptions): ChildProcess {
   args.push('-v', `${opts.workspacesDir}:/app/workspaces`);
   args.push('-v', `${opts.repo.hostPath}:${opts.repo.containerPath}:ro`);
 
-  // Writable overlays: shadow .shannon/ and .playwright/ inside the :ro repo with workspace-backed dirs
-  const workspacePath = path.join(opts.workspacesDir, opts.workspace);
-  args.push('-v', `${path.join(workspacePath, 'deliverables')}:${opts.repo.containerPath}/.shannon/deliverables`);
-  args.push('-v', `${path.join(workspacePath, 'scratchpad')}:${opts.repo.containerPath}/.shannon/scratchpad`);
-  args.push('-v', `${path.join(workspacePath, '.playwright-cli')}:${opts.repo.containerPath}/.shannon/.playwright-cli`);
-  args.push('-v', `${path.join(workspacePath, '.playwright')}:${opts.repo.containerPath}/.playwright`);
+  // Writable overlays: shadow .shannon/ and .playwright/ inside the :ro repo with workspace-backed
+  // dirs, nested under the run's INTERNAL_DIR. Container paths are unchanged.
+  const internalPath = path.join(opts.workspacesDir, opts.workspace, INTERNAL_DIR);
+  args.push('-v', `${path.join(internalPath, 'deliverables')}:${opts.repo.containerPath}/.shannon/deliverables`);
+  args.push('-v', `${path.join(internalPath, 'scratchpad')}:${opts.repo.containerPath}/.shannon/scratchpad`);
+  args.push('-v', `${path.join(internalPath, '.playwright-cli')}:${opts.repo.containerPath}/.shannon/.playwright-cli`);
+  args.push('-v', `${path.join(internalPath, '.playwright')}:${opts.repo.containerPath}/.playwright`);
 
   // Local mode: mount prompts for live editing
   if (opts.promptsDir) {
@@ -336,7 +338,7 @@ export function stopWorkers(): void {
   if (!workers) return;
 
   const ids = workers.split('\n').filter(Boolean);
-  console.log('Stopping worker containers...');
+  console.log('Stopping running scans...');
   execFileSync('docker', ['stop', ...ids], { stdio: 'inherit' });
 }
 

apps/cli/src/index.ts

@@ -9,9 +9,6 @@
  * in the current working directory.
  */
 
-import fs from 'node:fs';
-import path from 'node:path';
-import { fileURLToPath } from 'node:url';
 import { build } from './commands/build.js';
 import { logs } from './commands/logs.js';
 import { setup } from './commands/setup.js';
@@ -21,9 +18,7 @@ import { stop } from './commands/stop.js';
 import { uninstall } from './commands/uninstall.js';
 import { workspaces } from './commands/workspaces.js';
 import { getMode } from './mode.js';
-import { displaySplash } from './splash.js';
-
-const __dirname = path.dirname(fileURLToPath(import.meta.url));
+import { getVersion, getVersionLine } from './version.js';
 
 function blockSudo(): void {
   const isSudo = !!process.env.SUDO_USER;
@@ -44,16 +39,6 @@ function blockSudo(): void {
   process.exit(1);
 }
 
-function getVersion(): string {
-  try {
-    const pkgPath = path.join(__dirname, '..', 'package.json');
-    const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8')) as { version?: string };
-    return pkg.version || '1.0.0';
-  } catch {
-    return '1.0.0';
-  }
-}
-
 function showHelp(): void {
   const mode = getMode();
   const prefix = mode === 'local' ? './shannon' : 'npx @keygraph/shannon';
@@ -68,17 +53,17 @@ Usage:${
   ${prefix} setup                                       Configure credentials`
   }
   ${prefix} start --url <url> --repo <path> [options]   Start a pentest scan
-  ${prefix} stop [--clean]                               Stop all containers
+  ${prefix} stop [--clean] [--yes]                       Stop all running scans
   ${prefix} workspaces                                   List all workspaces
-  ${prefix} logs <workspace>                             Tail workflow log
-  ${prefix} status                                       Show running workers${
+  ${prefix} logs <workspace>                             Show a scan's live log
+  ${prefix} status                                       Show running scans${
     mode === 'local'
       ? `
   ${prefix} build [--no-cache]                           Build worker image`
       : `
-  ${prefix} uninstall                                    Remove ~/.shannon/ and all data`
+  ${prefix} uninstall [--yes]                            Remove ~/.shannon/ and all data`
   }
-  ${prefix} info                                         Show splash screen
+  ${prefix} version                                      Show version
   ${prefix} help                                         Show this help
 
 Options for 'start':
@@ -102,7 +87,7 @@ State directory: ./workspaces/`
     : `
 State directory: ~/.shannon/`
 }
-Monitor workflows at http://localhost:8233
+Monitor scans at http://localhost:8233
 `);
 }
 
@@ -209,7 +194,7 @@ switch (command) {
     break;
   }
   case 'stop':
-    stop(args.includes('--clean'));
+    stop(args.includes('--clean'), args.includes('--yes') || args.includes('-y'));
     break;
   case 'logs': {
     const workspaceId = args[1];
@@ -242,10 +227,12 @@ switch (command) {
       console.error('ERROR: uninstall is only available in npx mode.');
       process.exit(1);
     }
-    uninstall();
+    uninstall(args.includes('--yes') || args.includes('-y'));
     break;
-  case 'info':
-    displaySplash(getMode() === 'local' ? undefined : getVersion());
+  case 'version':
+  case '--version':
+  case '-v':
+    console.log(getVersionLine());
     break;
   case 'help':
   case '--help':

apps/cli/src/paths.ts

@@ -14,6 +14,38 @@ export interface MountPair {
   containerPath: string;
 }
 
+/**
+ * Hidden subdirectory inside each run directory that holds all internals
+ * (deliverables, logs, prompts, session state, browser artifacts). Keeps the
+ * run folder's top level clean so only the final report is visible. Must match
+ * INTERNAL_DIR in the worker package.
+ */
+export const INTERNAL_DIR = '.shannon';
+
+/**
+ * Filename of the human-facing final report surfaced at the run directory root.
+ * Must match FINAL_REPORT_FILENAME in the worker package.
+ */
+export const FINAL_REPORT_FILENAME = 'Security-Assessment-Report.md';
+
+/**
+ * Resolve a run-directory file (e.g. session.json, workflow.log), preferring the
+ * current INTERNAL_DIR location and falling back to the legacy run-root location
+ * so pre-restructure workspaces keep working. Returns the INTERNAL_DIR path when
+ * neither exists — the right default for new runs and error messages.
+ */
+export function resolveRunFile(runDir: string, filename: string): string {
+  const current = path.join(runDir, INTERNAL_DIR, filename);
+  if (fs.existsSync(current)) {
+    return current;
+  }
+  const legacy = path.join(runDir, filename);
+  if (fs.existsSync(legacy)) {
+    return legacy;
+  }
+  return current;
+}
+
 /**
  * Resolve --repo to absolute path and container mount.
  * Dev mode: bare names (no / or . prefix) check ./repos/<name> first.

apps/cli/src/splash.ts

@@ -1,14 +1,18 @@
 /**
  * Splash screen display — pure terminal output, no npm dependencies.
+ * Color escapes are gated on terminal support; the Unicode art is always kept.
  */
 
+import { supportsColor } from './tty.js';
+
 export function displaySplash(version?: string): void {
-  const GOLD = '\x1b[38;2;244;197;66m';
-  const CYAN = '\x1b[36;1m';
-  const WHITE = '\x1b[1;37m';
-  const GRAY = '\x1b[0;37m';
-  const YELLOW = '\x1b[1;33m';
-  const RESET = '\x1b[0m';
+  const color = supportsColor();
+  const GOLD = color ? '\x1b[38;2;244;197;66m' : '';
+  const CYAN = color ? '\x1b[36;1m' : '';
+  const WHITE = color ? '\x1b[1;37m' : '';
+  const GRAY = color ? '\x1b[0;37m' : '';
+  const YELLOW = color ? '\x1b[1;33m' : '';
+  const RESET = color ? '\x1b[0m' : '';
 
   const B = `${CYAN}\u2551${RESET}`;
   const S67 = ' '.repeat(67);

apps/cli/src/tty.ts

@@ -0,0 +1,34 @@
+/**
+ * Terminal capability detection — output coloring, cursor animation, and
+ * whether the user can be prompted interactively.
+ */
+
+/** True when stdout is a real terminal — safe for color, cursor moves, and spinners. */
+export function stdoutIsTerminal(): boolean {
+  return !!process.stdout.isTTY;
+}
+
+/** True when both stdin and stdout are terminals, so interactive prompts can run. */
+function isInteractive(): boolean {
+  return !!process.stdin.isTTY && !!process.stdout.isTTY;
+}
+
+/** True when color escapes should be emitted. NO_COLOR disables; FORCE_COLOR overrides (0/false/empty = off). */
+export function supportsColor(): boolean {
+  if (process.env.NO_COLOR !== undefined) return false;
+
+  const force = process.env.FORCE_COLOR;
+  if (force !== undefined) {
+    return force !== '0' && force !== 'false' && force !== '';
+  }
+
+  return stdoutIsTerminal();
+}
+
+/** Exit with a clear error when an interactive-only command has no terminal, instead of hanging on a prompt. */
+export function requireInteractive(command: string, alternative: string): void {
+  if (isInteractive()) return;
+  console.error(`ERROR: '${command}' needs an interactive terminal.`);
+  console.error(alternative);
+  process.exit(1);
+}

apps/cli/src/version.ts

@@ -0,0 +1,59 @@
+/**
+ * Version reporting — mode-aware.
+ *
+ * NPX mode:   the published package.json version (stamped by CI at release).
+ * Local mode: the git commit SHA of the checked-out clone (`git-<full-sha>`).
+ *             A clone has no meaningful semver, so the commit is the honest identifier.
+ */
+
+import { execFileSync } from 'node:child_process';
+import fs from 'node:fs';
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { getMode } from './mode.js';
+
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+
+function readPackageVersion(): string {
+  try {
+    const pkgPath = path.join(__dirname, '..', 'package.json');
+    const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8')) as { version?: string };
+    return pkg.version || '1.0.0';
+  } catch {
+    return '1.0.0';
+  }
+}
+
+/** Run a git command in the CLI's own repo; returns trimmed stdout or null on any failure. */
+function git(...args: string[]): string | null {
+  try {
+    return execFileSync('git', args, { cwd: __dirname, encoding: 'utf-8', stdio: ['ignore', 'pipe', 'ignore'] }).trim();
+  } catch {
+    return null;
+  }
+}
+
+function readGitSha(): string | null {
+  return git('rev-parse', 'HEAD');
+}
+
+/**
+ * Version identifier. NPX: package.json version. Local: `git-<full-sha>`,
+ * falling back to the package version if git is unavailable.
+ */
+export function getVersion(): string {
+  if (getMode() !== 'local') return readPackageVersion();
+
+  const sha = readGitSha();
+  if (!sha) return readPackageVersion();
+
+  return `git-${sha}`;
+}
+
+/**
+ * Human-facing version line printed by `--version`.
+ * NPX: `shannon <version>`. Local: `shannon git-<full-sha>`.
+ */
+export function getVersionLine(): string {
+  return `shannon ${getVersion()}`;
+}

apps/worker/src/audit/utils.ts

@@ -12,7 +12,7 @@
  */
 
 import path from 'node:path';
-import { WORKSPACES_DIR } from '../paths.js';
+import { INTERNAL_DIR, WORKSPACES_DIR } from '../paths.js';
 import { ensureDirectory } from '../utils/file-io.js';
 
 export type { SessionMetadata } from '../types/audit.js';
@@ -35,8 +35,9 @@ export function generateSessionIdentifier(sessionMetadata: SessionMetadata): str
 }
 
 /**
- * Generate path to audit log directory for a session
- * Uses custom outputPath if provided, otherwise defaults to WORKSPACES_DIR
+ * Generate path to a run directory for a session (its top level).
+ * Uses custom outputPath if provided, otherwise defaults to WORKSPACES_DIR.
+ * Only the final report lives here; all internals live under INTERNAL_DIR.
  */
 export function generateAuditPath(sessionMetadata: SessionMetadata): string {
   const sessionIdentifier = generateSessionIdentifier(sessionMetadata);
@@ -44,6 +45,14 @@ export function generateAuditPath(sessionMetadata: SessionMetadata): string {
   return path.join(baseDir, sessionIdentifier);
 }
 
+/**
+ * Generate path to the hidden internals directory inside a run directory.
+ * Holds logs, prompts, session state, deliverables, and browser artifacts.
+ */
+export function generateInternalPath(sessionMetadata: SessionMetadata): string {
+  return path.join(generateAuditPath(sessionMetadata), INTERNAL_DIR);
+}
+
 /**
  * Generate path to agent log file
  */
@@ -53,25 +62,25 @@ export function generateLogPath(
   timestamp: number,
   attemptNumber: number,
 ): string {
-  const auditPath = generateAuditPath(sessionMetadata);
+  const internalPath = generateInternalPath(sessionMetadata);
   const filename = `${timestamp}_${agentName}_attempt-${attemptNumber}.log`;
-  return path.join(auditPath, 'agents', filename);
+  return path.join(internalPath, 'agents', filename);
 }
 
 /**
  * Generate path to prompt snapshot file
  */
 export function generatePromptPath(sessionMetadata: SessionMetadata, agentName: string): string {
-  const auditPath = generateAuditPath(sessionMetadata);
-  return path.join(auditPath, 'prompts', `${agentName}.md`);
+  const internalPath = generateInternalPath(sessionMetadata);
+  return path.join(internalPath, 'prompts', `${agentName}.md`);
 }
 
 /**
  * Generate path to session.json file
  */
 export function generateSessionJsonPath(sessionMetadata: SessionMetadata): string {
-  const auditPath = generateAuditPath(sessionMetadata);
-  return path.join(auditPath, 'session.json');
+  const internalPath = generateInternalPath(sessionMetadata);
+  return path.join(internalPath, 'session.json');
 }
 
 /**
@@ -79,29 +88,28 @@ export function generateSessionJsonPath(sessionMetadata: SessionMetadata): strin
  * validator and consumed by downstream agents via `_shared-session.txt`.
  */
 export function authStateFile(sessionMetadata: SessionMetadata): string {
-  return path.join(generateAuditPath(sessionMetadata), 'auth-state.json');
+  return path.join(generateInternalPath(sessionMetadata), 'auth-state.json');
 }
 
 /**
  * Generate path to workflow.log file
  */
 export function generateWorkflowLogPath(sessionMetadata: SessionMetadata): string {
-  const auditPath = generateAuditPath(sessionMetadata);
-  return path.join(auditPath, 'workflow.log');
+  const internalPath = generateInternalPath(sessionMetadata);
+  return path.join(internalPath, 'workflow.log');
 }
 
 /**
- * Initialize audit directory structure for a session
- * Creates: workspaces/{sessionId}/, agents/, prompts/, deliverables/
+ * Initialize audit directory structure for a session.
+ * Creates: workspaces/{sessionId}/.shannon/{agents,prompts}. The deliverables,
+ * scratchpad, and browser dirs are created host-side and bind-mounted in.
  */
 export async function initializeAuditStructure(sessionMetadata: SessionMetadata): Promise<void> {
-  const auditPath = generateAuditPath(sessionMetadata);
-  const agentsPath = path.join(auditPath, 'agents');
-  const promptsPath = path.join(auditPath, 'prompts');
-  const deliverablesPath = path.join(auditPath, 'deliverables');
+  const internalPath = generateInternalPath(sessionMetadata);
+  const agentsPath = path.join(internalPath, 'agents');
+  const promptsPath = path.join(internalPath, 'prompts');
 
-  await ensureDirectory(auditPath);
+  await ensureDirectory(internalPath);
   await ensureDirectory(agentsPath);
   await ensureDirectory(promptsPath);
-  await ensureDirectory(deliverablesPath);
 }

apps/worker/src/audit/workflow-logger.ts

@@ -80,7 +80,7 @@ export class WorkflowLogger {
   private async writeHeader(): Promise<void> {
     const lines = [
       `================================================================================`,
-      `Shannon Pentest - Workflow Log`,
+      `Shannon Pentest - Scan Log`,
       `================================================================================`,
       `Workflow ID: ${this.workflowId ?? this.sessionMetadata.id}`,
       `Target URL:  ${this.sessionMetadata.webUrl}`,
@@ -337,7 +337,7 @@ export class WorkflowLogger {
     const lines: string[] = [
       '',
       '================================================================================',
-      `Workflow ${status}`,
+      `Scan ${status}`,
       '────────────────────────────────────────',
       `Workflow ID: ${this.workflowId ?? this.sessionMetadata.id}`,
       `Status:      ${summary.status}`,

apps/worker/src/paths.ts

@@ -15,6 +15,36 @@ export const DEFAULT_DELIVERABLES_SUBDIR = '.shannon/deliverables';
 /** Default audit log directory */
 export const DEFAULT_AUDIT_DIR = './workspaces';
 
+/**
+ * Hidden subdirectory inside each run directory that holds all internals
+ * (logs, prompts, session state, deliverables, browser artifacts). Keeps the
+ * run folder's top level clean so only the final report is visible.
+ */
+export const INTERNAL_DIR = '.shannon';
+
+/** Filename of the assembled report inside the deliverables dir (internal, source of the surfaced copy) */
+export const ASSEMBLED_REPORT_FILENAME = 'comprehensive_security_assessment_report.md';
+
+/** Filename of the human-facing final report surfaced at the run directory root */
+export const FINAL_REPORT_FILENAME = 'Security-Assessment-Report.md';
+
+/**
+ * Resolve the session.json path for a run directory, preferring the current
+ * `.shannon/` location and falling back to the legacy run-root location so
+ * pre-restructure workspaces remain listable and resumable.
+ */
+export function resolveSessionJsonPath(runDir: string): string {
+  const current = path.join(runDir, INTERNAL_DIR, 'session.json');
+  if (fs.existsSync(current)) {
+    return current;
+  }
+  const legacy = path.join(runDir, 'session.json');
+  if (fs.existsSync(legacy)) {
+    return legacy;
+  }
+  return current;
+}
+
 /**
  * Resolve the deliverables directory for a given repoPath and optional subdir override.
  * @param repoPath - Absolute path to the target repository

apps/worker/src/services/index.ts

@@ -20,4 +20,4 @@ export type { ContainerDependencies } from './container.js';
 export { Container, getContainer, getOrCreateContainer, removeContainer, setContainerFactory } from './container.js';
 export { ExploitationCheckerService } from './exploitation-checker.js';
 export { loadPrompt } from './prompt-manager.js';
-export { assembleFinalReport, injectModelIntoReport } from './reporting.js';
+export { assembleFinalReport, copyReportToRunRoot, injectModelIntoReport } from './reporting.js';

apps/worker/src/services/reporting.ts

@@ -5,7 +5,7 @@
 // as published by the Free Software Foundation.
 
 import { fs, path } from 'zx';
-import { deliverablesDir } from '../paths.js';
+import { ASSEMBLED_REPORT_FILENAME, deliverablesDir, FINAL_REPORT_FILENAME, resolveSessionJsonPath } from '../paths.js';
 import type { ActivityLogger } from '../types/activity-logger.js';
 import { ErrorCode } from '../types/errors.js';
 import { PentestError } from './error-handling.js';
@@ -68,7 +68,7 @@ export async function assembleFinalReport(
   }
 
   const finalContent = sections.join('\n\n');
-  const finalReportPath = path.join(dir, 'comprehensive_security_assessment_report.md');
+  const finalReportPath = path.join(dir, ASSEMBLED_REPORT_FILENAME);
 
   try {
     await fs.ensureDir(dir);
@@ -97,7 +97,7 @@ export async function injectModelIntoReport(
   logger: ActivityLogger,
 ): Promise<void> {
   // 1. Read session.json to get model information
-  const sessionJsonPath = path.join(outputPath, 'session.json');
+  const sessionJsonPath = resolveSessionJsonPath(outputPath);
 
   if (!(await fs.pathExists(sessionJsonPath))) {
     logger.warn('session.json not found, skipping model injection');
@@ -129,10 +129,7 @@ export async function injectModelIntoReport(
   logger.info(`Injecting model info into report: ${modelStr}`);
 
   // 3. Read the final report
-  const reportPath = path.join(
-    deliverablesDir(repoPath, deliverablesSubdir),
-    'comprehensive_security_assessment_report.md',
-  );
+  const reportPath = path.join(deliverablesDir(repoPath, deliverablesSubdir), ASSEMBLED_REPORT_FILENAME);
 
   if (!(await fs.pathExists(reportPath))) {
     logger.warn('Final report not found, skipping model injection');
@@ -167,3 +164,26 @@ export async function injectModelIntoReport(
   // 5. Write modified report back
   await fs.writeFile(reportPath, reportContent);
 }
+
+/**
+ * Surface the assembled report at the run directory's top level as the single
+ * human-facing deliverable, so a customer opening the run folder sees only the
+ * report. The source stays in the deliverables dir (git-checkpointed, used by resume).
+ */
+export async function copyReportToRunRoot(
+  repoPath: string,
+  deliverablesSubdir: string | undefined,
+  runDir: string,
+  logger: ActivityLogger,
+): Promise<void> {
+  const source = path.join(deliverablesDir(repoPath, deliverablesSubdir), ASSEMBLED_REPORT_FILENAME);
+
+  if (!(await fs.pathExists(source))) {
+    logger.warn(`Final report not found, skipping ${FINAL_REPORT_FILENAME}`);
+    return;
+  }
+
+  const destination = path.join(runDir, FINAL_REPORT_FILENAME);
+  await fs.copy(source, destination, { overwrite: true });
+  logger.info(`Surfaced report at ${destination}`);
+}

apps/worker/src/temporal/activities.ts

@@ -22,10 +22,10 @@ import { writePlaywrightStealthConfig } from '../ai/playwright-config-writer.js'
 import { writeUserSettingsForCodePathAvoids } from '../ai/settings-writer.js';
 import { AuditSession } from '../audit/index.js';
 import type { ResumeAttempt } from '../audit/metrics-tracker.js';
-import { authStateFile, generateSessionJsonPath, type SessionMetadata } from '../audit/utils.js';
+import { authStateFile, generateAuditPath, generateSessionJsonPath, type SessionMetadata } from '../audit/utils.js';
 import type { WorkflowSummary } from '../audit/workflow-logger.js';
 import type { CheckpointContext } from '../interfaces/checkpoint-provider.js';
-import { DEFAULT_DELIVERABLES_SUBDIR, deliverablesDir } from '../paths.js';
+import { DEFAULT_DELIVERABLES_SUBDIR, deliverablesDir, resolveSessionJsonPath } from '../paths.js';
 import { getContainer, getOrCreateContainer, removeContainer } from '../services/container.js';
 import { classifyErrorForTemporal, PentestError } from '../services/error-handling.js';
 import { ExploitationCheckerService } from '../services/exploitation-checker.js';
@@ -33,7 +33,7 @@ import { renderFindingsFromQueues } from '../services/findings-renderer.js';
 import { executeGitCommandWithRetry } from '../services/git-manager.js';
 import { runPreflightChecks } from '../services/preflight.js';
 import type { ExploitationDecision, VulnType } from '../services/queue-validation.js';
-import { assembleFinalReport, injectModelIntoReport } from '../services/reporting.js';
+import { assembleFinalReport, copyReportToRunRoot, injectModelIntoReport } from '../services/reporting.js';
 import { validateAuthentication } from '../services/validate-authentication.js';
 import { AGENTS } from '../session-manager.js';
 import type { AgentName } from '../types/agents.js';
@@ -756,8 +756,8 @@ export async function loadResumeState(
   expectedRepoPath: string,
   deliverablesSubdir?: string,
 ): Promise<ResumeState> {
-  // 1. Validate workspace exists
-  const sessionPath = path.join('./workspaces', workspaceName, 'session.json');
+  // 1. Validate workspace exists (prefers .shannon/, falls back to legacy run-root layout)
+  const sessionPath = resolveSessionJsonPath(path.join('./workspaces', workspaceName));
 
   const exists = await fileExists(sessionPath);
   if (!exists) {
@@ -1055,7 +1055,23 @@ export async function logWorkflowComplete(input: ActivityInput, summary: Workflo
   // 5. Write completion entry to workflow.log
   await auditSession.logWorkflowComplete(cumulativeSummary);
 
-  // 6. Drop the authenticated browser session
+  // 6. Surface the final report at the run root. Done here (not in the report phase)
+  // so it also runs when a resume skips an already-complete report phase.
+  if (summary.status === 'completed') {
+    try {
+      await copyReportToRunRoot(
+        input.repoPath,
+        input.deliverablesSubdir,
+        generateAuditPath(sessionMetadata),
+        createActivityLogger(),
+      );
+    } catch (error) {
+      const detail = error instanceof Error ? error.message : String(error);
+      console.warn(`Failed to surface report at run root: ${detail}`);
+    }
+  }
+
+  // 7. Drop the authenticated browser session
   try {
     await fs.rm(authStateFile(sessionMetadata), { force: true });
   } catch (error) {
@@ -1063,7 +1079,7 @@ export async function logWorkflowComplete(input: ActivityInput, summary: Workflo
     console.warn(`Failed to clean up auth-state.json: ${detail}`);
   }
 
-  // 7. Clean up container
+  // 8. Clean up container
   removeContainer(workflowId);
 }
 

apps/worker/src/temporal/worker.ts

@@ -35,7 +35,7 @@ import { bundleWorkflowCode, NativeConnection, Worker } from '@temporalio/worker
 import dotenv from 'dotenv';
 import { sanitizeHostname } from '../audit/utils.js';
 import { parseConfig } from '../config-parser.js';
-import { deliverablesDir } from '../paths.js';
+import { ASSEMBLED_REPORT_FILENAME, deliverablesDir, FINAL_REPORT_FILENAME, resolveSessionJsonPath } from '../paths.js';
 import type { PipelineConfig, VulnClass } from '../types/config.js';
 import { fileExists, readJson } from '../utils/file-io.js';
 import * as activities from './activities.js';
@@ -171,7 +171,7 @@ interface WorkspaceResolution {
 }
 
 async function terminateExistingWorkflows(client: Client, workspaceName: string): Promise<string[]> {
-  const sessionPath = path.join('./workspaces', workspaceName, 'session.json');
+  const sessionPath = resolveSessionJsonPath(path.join('./workspaces', workspaceName));
 
   if (!(await fileExists(sessionPath))) {
     throw new Error(`Workspace not found: ${workspaceName}\n` + `Expected path: ${sessionPath}`);
@@ -192,16 +192,16 @@ async function terminateExistingWorkflows(client: Client, workspaceName: string)
       const description = await handle.describe();
 
       if (description.status.name === 'RUNNING') {
-        console.log(`Terminating running workflow: ${wfId}`);
+        console.log(`Terminating running scan: ${wfId}`);
         await handle.terminate('Superseded by resume workflow');
         terminated.push(wfId);
         console.log(`Terminated: ${wfId}`);
       } else {
-        console.log(`Workflow already ${description.status.name}: ${wfId}`);
+        console.log(`Scan already ${description.status.name}: ${wfId}`);
       }
     } catch (error) {
       if (error instanceof WorkflowNotFoundError) {
-        console.log(`Workflow not found (already cleaned up): ${wfId}`);
+        console.log(`Scan not found (already cleaned up): ${wfId}`);
       } else {
         console.log(`Failed to terminate ${wfId}: ${error}`);
       }
@@ -224,7 +224,7 @@ async function resolveWorkspace(client: Client, args: CliArgs): Promise<Workspac
   }
 
   const workspace = args.resumeFromWorkspace;
-  const sessionPath = path.join('./workspaces', workspace, 'session.json');
+  const sessionPath = resolveSessionJsonPath(path.join('./workspaces', workspace));
   const workspaceExists = await fileExists(sessionPath);
 
   if (workspaceExists) {
@@ -233,7 +233,7 @@ async function resolveWorkspace(client: Client, args: CliArgs): Promise<Workspac
 
     const terminatedWorkflows = await terminateExistingWorkflows(client, workspace);
     if (terminatedWorkflows.length > 0) {
-      console.log(`Terminated ${terminatedWorkflows.length} previous workflow(s)\n`);
+      console.log(`Terminated ${terminatedWorkflows.length} previous scan(s)\n`);
     }
 
     const session = await readJson<SessionJson>(sessionPath);
@@ -355,7 +355,9 @@ async function waitForWorkflowResult(
 
       if (workspace.isResume) {
         try {
-          const session = await readJson<SessionJson>(path.join('./workspaces', workspace.sessionId, 'session.json'));
+          const session = await readJson<SessionJson>(
+            resolveSessionJsonPath(path.join('./workspaces', workspace.sessionId)),
+          );
           console.log(`Cumulative cost: $${session.metrics.total_cost_usd.toFixed(4)}`);
         } catch {
           // Non-fatal
@@ -393,6 +395,12 @@ function copyDeliverables(repoPath: string, outputPath: string): void {
     fs.cpSync(src, dest, { recursive: true });
   }
 
+  // Surface the report under its human-facing name alongside the raw deliverables
+  const assembledReport = path.join(outputDir, ASSEMBLED_REPORT_FILENAME);
+  if (fs.existsSync(assembledReport)) {
+    fs.copyFileSync(assembledReport, path.join(outputPath, FINAL_REPORT_FILENAME));
+  }
+
   console.log(`Copied ${files.length} deliverable(s) to ${outputPath}`);
 }
 
@@ -412,7 +420,7 @@ async function run(): Promise<void> {
 
   try {
     // 3. Bundle workflows and create worker on per-invocation task queue
-    console.log('Bundling workflows...');
+    console.log('Preparing scan...');
     const workflowBundle = await bundleWorkflowCode({
       workflowsPath: path.join(__dirname, 'workflows.js'),
     });

apps/worker/src/temporal/workspaces.ts

@@ -20,7 +20,7 @@
 
 import fs from 'node:fs/promises';
 import path from 'node:path';
-import { WORKSPACES_DIR as DEFAULT_WORKSPACES_DIR } from '../paths.js';
+import { WORKSPACES_DIR as DEFAULT_WORKSPACES_DIR, resolveSessionJsonPath } from '../paths.js';
 
 interface SessionJson {
   session: {
@@ -82,7 +82,7 @@ async function listWorkspaces(): Promise<void> {
   const workspaces: WorkspaceInfo[] = [];
 
   for (const entry of entries) {
-    const sessionPath = path.join(workspacesDir, entry, 'session.json');
+    const sessionPath = resolveSessionJsonPath(path.join(workspacesDir, entry));
     try {
       const content = await fs.readFile(sessionPath, 'utf8');
       const data = JSON.parse(content) as SessionJson;

docs/ai-providers.md

@@ -98,7 +98,7 @@ Shannon supports pointing the SDK at an Anthropic-compatible endpoint with `ANTH
 > [!IMPORTANT]
 > Only Claude models are officially supported. Shannon's evaluations, internal testing, and agent harness are optimized for Claude. Smaller or alternative models, including non-Claude models routed through a proxy, may not reliably follow Shannon's instructions or tool-use constraints. Use them at your own risk.
 
-The experimental `claude-code-router` integration is being removed. If you rely on it, migrate to an Anthropic-compatible proxy such as LiteLLM before upgrading.
+The experimental `claude-code-router` integration has been removed. If you previously relied on it, migrate to an Anthropic-compatible proxy such as LiteLLM.
 
 Run `npx @keygraph/shannon setup` and select **Custom Base URL**, or export variables directly:
 

docs/development.md

@@ -61,6 +61,7 @@ Monitor progress:
 ```bash
 npx @keygraph/shannon logs <workspace>
 npx @keygraph/shannon status
+npx @keygraph/shannon version
 ```
 
 Source-build equivalents:
@@ -68,6 +69,7 @@ Source-build equivalents:
 ```bash
 ./shannon logs <workspace>
 ./shannon status
+./shannon version
 ```
 
 Open the Temporal Web UI for detailed monitoring:
@@ -80,15 +82,15 @@ Stop Shannon:
 
 ```bash
 npx @keygraph/shannon stop
-npx @keygraph/shannon stop --clean
-npx @keygraph/shannon uninstall
+npx @keygraph/shannon stop --clean       # confirms first; add --yes (or -y) to skip
+npx @keygraph/shannon uninstall          # confirms first; add --yes (or -y) to skip
 ```
 
 Source-build equivalents:
 
 ```bash
 ./shannon stop
-./shannon stop --clean
+./shannon stop --clean                   # add --yes (or -y) to skip the confirmation
 ```
 
 Usage examples:
@@ -132,14 +134,16 @@ Results are saved to the workspaces directory:
 
 Use `-o <path>` to copy deliverables to a custom output directory after a run completes.
 
-Output structure:
+Output structure — the run directory's top level holds only the final report; everything else is nested under a hidden `.shannon/` directory:
 
 ```text
 workspaces/{hostname}_{sessionId}/
-|-- session.json
-|-- workflow.log
-|-- agents/
-|-- prompts/
-`-- deliverables/
-    `-- comprehensive_security_assessment_report.md
+|-- Security-Assessment-Report.md   # the final report (the deliverable)
+`-- .shannon/                       # internals
+    |-- deliverables/               # report source, per-phase analysis, queues
+    |-- agents/                     # per-agent logs
+    |-- prompts/                    # rendered prompts
+    |-- scratchpad/                 # screenshots, scripts
+    |-- session.json                # resume state
+    `-- workflow.log
 ```

docs/workspaces.md

@@ -11,6 +11,7 @@ Shannon uses workspaces to store scan state, logs, prompts, and deliverables. Wo
 - Use `-w <name>` to give a run a custom name.
 - To resume a run, pass the same workspace name with `-w`.
 - Each agent's progress is checkpointed so resumed runs can skip completed work.
+- The final report is surfaced at the workspace root as `Security-Assessment-Report.md`. Run internals — deliverables, logs, prompts, and session state — live under a hidden `.shannon/` directory.
 
 > [!NOTE]
 > The URL must match the original workspace URL when resuming. Shannon rejects mismatched URLs to prevent cross-target contamination.

llms-full.txt

@@ -322,6 +322,7 @@ Monitor progress:
 ```bash
 npx @keygraph/shannon logs <workspace>
 npx @keygraph/shannon status
+npx @keygraph/shannon version
 ```
 
 Source-build equivalents:
@@ -329,6 +330,7 @@ Source-build equivalents:
 ```bash
 ./shannon logs <workspace>
 ./shannon status
+./shannon version
 ```
 
 Open the Temporal Web UI for detailed monitoring:
@@ -341,15 +343,15 @@ Stop Shannon:
 
 ```bash
 npx @keygraph/shannon stop
-npx @keygraph/shannon stop --clean
-npx @keygraph/shannon uninstall
+npx @keygraph/shannon stop --clean       # confirms first; add --yes (or -y) to skip
+npx @keygraph/shannon uninstall          # confirms first; add --yes (or -y) to skip
 ```
 
 Source-build equivalents:
 
 ```bash
 ./shannon stop
-./shannon stop --clean
+./shannon stop --clean                   # add --yes (or -y) to skip the confirmation
 ```
 
 Usage examples:
@@ -393,16 +395,18 @@ Results are saved to the workspaces directory:
 
 Use `-o <path>` to copy deliverables to a custom output directory after a run completes.
 
-Output structure:
+Output structure — the run directory's top level holds only the final report; everything else is nested under a hidden `.shannon/` directory:
 
 ```text
 workspaces/{hostname}_{sessionId}/
-|-- session.json
-|-- workflow.log
-|-- agents/
-|-- prompts/
-`-- deliverables/
-    `-- comprehensive_security_assessment_report.md
+|-- Security-Assessment-Report.md   # the final report (the deliverable)
+`-- .shannon/                       # internals
+    |-- deliverables/               # report source, per-phase analysis, queues
+    |-- agents/                     # per-agent logs
+    |-- prompts/                    # rendered prompts
+    |-- scratchpad/                 # screenshots, scripts
+    |-- session.json                # resume state
+    `-- workflow.log
 ```
 
 ---
@@ -665,7 +669,7 @@ Shannon supports pointing the SDK at an Anthropic-compatible endpoint with `ANTH
 > [!IMPORTANT]
 > Only Claude models are officially supported. Shannon's evaluations, internal testing, and agent harness are optimized for Claude. Smaller or alternative models, including non-Claude models routed through a proxy, may not reliably follow Shannon's instructions or tool-use constraints. Use them at your own risk.
 
-The experimental `claude-code-router` integration is being removed. If you rely on it, migrate to an Anthropic-compatible proxy such as LiteLLM before upgrading.
+The experimental `claude-code-router` integration has been removed. If you previously relied on it, migrate to an Anthropic-compatible proxy such as LiteLLM.
 
 Run `npx @keygraph/shannon setup` and select **Custom Base URL**, or export variables directly:
 
@@ -793,6 +797,7 @@ Shannon uses workspaces to store scan state, logs, prompts, and deliverables. Wo
 - Use `-w <name>` to give a run a custom name.
 - To resume a run, pass the same workspace name with `-w`.
 - Each agent's progress is checkpointed so resumed runs can skip completed work.
+- The final report is surfaced at the workspace root as `Security-Assessment-Report.md`. Run internals — deliverables, logs, prompts, and session state — live under a hidden `.shannon/` directory.
 
 > [!NOTE]
 > The URL must match the original workspace URL when resuming. Shannon rejects mismatched URLs to prevent cross-target contamination.