feat: Shannon 3.0 Agentic SAST (#433)

* feat(worker): add agentic static analysis

Add the ten-stage Agentic SAST pipeline, confined repository tools, model runtime, prompt templates, and SARIF export.

Make retries, repair sessions, reduced coverage, usage accounting, and model-output drift durable across Temporal replay and resume. Keep retry diagnostics in their actionable closed vocabulary. Package the Mantis-derived license material with the prompts that require it.

* feat(worker): deduplicate static and runtime findings before exploitation

Parse Agentic SAST SARIF into typed observations, enrich and route those observations, and reconcile them with pentest findings before exploitation.

Publish deterministic exploitation queues with stable lineage, exact-path Git commits, retry-safe manifests, named drop reasons, and confined task formation. Reject duplicate producer IDs before commit and adopt either legal provenance shape after a lost acknowledgement.

* feat(config)!: replace vuln_classes with agentic_sast

Wire Agentic SAST and reconciliation into the main pipeline, persist their durable state, and add the Miscellaneous finding and exploitation lane.

Make scan completion, cancellation, partial outcomes, resume identity, and report recovery use the integrated final workflow contract. Introduce the atomic finalization, ordering, renumbering, compaction, and output services that workflow calls. Keep completed Miscellaneous work and report drafts idempotent across resume, preserve public main's default-on exploit SARIF behavior, and describe stage-fallback candidates without claiming they were exported.

BREAKING CHANGE: `vuln_classes` has been removed. Configs containing it now fail validation, and all five core pentest classes run on every scan.

Workspaces created by Shannon 2.x cannot be resumed. Finish or discard in-flight scans before upgrading, then start a new workspace name.

* perf: overlap static analysis and the Miscellaneous lane with the pentest

Run Agentic SAST alongside vulnerability analysis and run Miscellaneous exploitation alongside the specialist exploitation lanes.

Keep reconciliation dependent on the completed static-analysis result while preserving parallel work everywhere that has no data dependency.

* feat(cli)!: default the scan target and add a JSON error contract

List local scans, resolve the active or most recent workspace automatically, and make logs, status, and stop use one canonical scan identity.

Add stable machine-readable failures, richer status output, explicit help errors, and seven-day Temporal retention. Treat absent Temporal pending-activity failures as absent whether the decoder represents them as `null` or missing.

BREAKING CHANGE: `status --json` now returns a fixed `failureMessage`. Read `partialReasons`, `agenticSast`, and `workflow.log` for diagnostic detail.

* feat(logging): trace tool calls and write a log per agent

Record complete tool-call arguments in the workflow log and project each agent's events into its own durable log.

Add agent listing and agent-specific log tailing while preserving byte-exact output and draining log handles before
activities return.

* feat(worker): standardize severity and reporting guidance in exploit prompts

Give every exploit agent the same status, confidence, severity-reasoning, report-writing, credential-handling, and
scope contract.

Apply the same task-formation and SAST-enrichment procedure to the Miscellaneous lane.

* feat(worker): disclose scan coverage and make reporting auditable

Build on the retry-safe finalization foundation to preserve correct identities, source locations, scan dates,
partial-coverage limitations, and consistent report JSON, Markdown, SARIF, and PDF output.

Report Agentic SAST, reconciliation wall-clock time, stage usage, retry spend, and background work without duplicate
or hardcoded totals. Keep report findings canonical, drop cross-class restatements, name enrichment losses, and render
the executive-summary narrative in the PDF.

* chore(license): attribute Mantis and Pi and refresh the docs

Add the final Mantis and Pi notices, license copies, acknowledgements, and residual copyright updates.

Update the README, maintained documentation, contributor guidance, and hand-maintained mirrors to describe Agentic
SAST, reconciliation, the Miscellaneous lane, current CLI behavior, and the final release contract. Correct stale
workspace and container guidance and annotate long-standing internals for maintainers.

* fix(logging): treat a slash as a word separator in agent labels

* feat(cli)!: rebuild scan status around model work

- show Capella stages beneath the concurrent Agentic SAST phase
- attach reconciliation time to the class row it feeds
- hide completed bookkeeping and the duplicate miscellaneous wrapper
- carry validated child-workflow progress into durable parent state
- derive the terminal tree and status JSON from the same phase shape

BREAKING CHANGE: `status --json` replaces phase `parallel` with `children` and `meta`, adds phase summaries and notes plus agent attachment fields, and removes the `analysis-engines` and `operational-work` phases.

* fix(report): drop the empty Critical Findings section from the PDF summary

* fix(sast): align Capella export with the submit-time code-path contract

The export gate required every code_paths entry to be file:line, but submit only
requires the primary sink to be file:line and accepts bare trace steps. A single
malformed trace step therefore dropped an otherwise-valid finding at export.

- add isValidPrimaryCodePath as the one shared primary-sink contract
- validate only the primary at export; buildResult already drops unusable steps
- route the submit-time validator through the same helper so the two cannot drift

* feat(sast): tolerate hygiene-only Capella reductions instead of going partial

A reduction only makes a run partial when it loses real coverage or a whole
finding. Malformed model output, salvaged turn-limit work, and rejected duplicate
verdicts are recorded as evidence but no longer flip the run to partial.

- add reductionIsTolerable: partial only when genuine-loss counts are nonzero
- drive runCapella's partial reasons and display coverage off non-tolerable ones
- keep every reduction in agenticSast.reductions so nothing is lost as evidence

* feat(logging): record the provider reason for a failed agent turn

A failed provider turn collapsed to AGENT_EXECUTION_FAILED/unknown with the
underlying reason discarded, so a model-side rejection or safeguard was
indistinguishable from a transport fault in the error log.

- add safeProviderTurnDetails: write bounded, non-sensitive fields (provider,
  model, responseId, stop reason, tool-in-flight, category, retryable) to error.log
- gate a sanitized errorMessage snippet behind SHANNON_DEBUG_PROVIDER_ERRORS, off by default
- forward SHANNON_DEBUG_PROVIDER_ERRORS from the CLI into the worker container

* fix(cli): keep shannon logs tailing through a Temporal blip

- End the interactive tail on the log's own terminal marker or Ctrl-C, so a
  transient Temporal outage no longer aborts the command with exit 1.
- Rebuild the memoized Temporal client after a failed poll: a wedged gRPC
  channel was cached forever, so "retrying…" could never reconnect.
- Keep start --follow (CI) bounded — a genuinely dead Temporal still fails
  the run instead of hanging.

* fix(worker): correct PDF finding reporting

- Render OWASP category, authentication state, and remediation
- Omit the redundant per-finding exploited status
- Preserve canonical category and field ordering across report modes
- Continue Proof of Impact numbering across embedded code blocks
- Wrap long PDF code lines without changing canonical report content

* fix: attribute a reconciliation failure to exploitation only

- Stop marking a class's vulnerability-analysis agent failed when that agent
  succeeded and only reconciliation failed; the status tree now renders the
  analysis row completed and the exploitation row failed
- Consume the worker's failedReconciliations signal in the CLI, which the
  mirrored PipelineState already declared but never read
- Correct the class_reconciliation_failed message, which claimed the class's
  analysis results were still in the report when the class is excluded from it

* fix(pi): give each task sub-session its own resource loader to prevent stale extension ctx

* fix(prompts): scope exploit agents to in-band proof, mark OOB-only findings blocked

* fix(cli): reject a shell credential that shadows a gateway config.toml key

* fix(cli): make scan shutdown verifiable

- preselect and persist workflow identity before worker launch
- cancel first, then verify bounded Temporal termination
- reconcile Docker workers with Temporal open workflows
- fail closed on stale images and unavailable lifecycle state
- mark cancellation only after confirmed shutdown

* feat(cli): prompt for setup on a bare npx invocation with no credentials

* fix(cli): don't blame anthropic when no credentials are configured at all

* chore(release): bump beta base version to 3.0.0

* feat(cli): show a 'start your first scan' box in help on a TTY

* docs: refresh README and platform overview for Shannon 3.0

- lead with the 3.0 launch note and rewrite key capabilities around security
  code analysis, the rebuilt terminal experience, native CI/CD, and PDF/SARIF
- recast the editions table as Shannon Open Source against the Keygraph
  Enterprise Platform, stating open source is not a trial edition
- rewrite the platform overview around exhaustive agentic SAST, canonical
  findings, automated remediation, targeted verification, and governance
- add five product screenshots under assets/keygraph-platform/, referenced
  relative to docs/

* docs: add the Shannon naming section and swap in the 3.0 demo GIF

- explain the Claude Shannon information-theory origin under "What is Shannon?"
- point "Shannon in Action" at the 3.0 recording in assets/Shannon3GIF.gif

Both taken from the README half of #438.

* docs: document CI/CD integrations and the reconciled analysis pipeline

- add a CI/CD Integrations section covering the official GitHub Action and
  GitLab component, pipeline artifacts, and exploit-only severity gates
- redraw the architecture section as a Mermaid flow: agentic code analysis
  and recon feed finding reconciliation, then exploitation and reporting
- describe open-source code analysis as a multi-stage agentic workflow and
  reserve parsed-code CPGs and exhaustive verification for Enterprise
- sharpen the privacy wording: results stay local, but model requests carry
  source context to whichever endpoint you configure
- drop the "not recommended" framing on local models and add a section on
  why Shannon complements rather than replaces human pentesters
- regenerate llms-full.txt from the updated README and docs

* docs: add the Photoview benchmark across three models

- Add a "Shannon in Action" table for Photoview 2.4.0 runs on
  DeepSeek v4 Flash, Grok 4.6, and Claude Opus 5, each linking its
  PDF report and SARIF output
- Store the per-model reports under benchmark/
- Link the (forthcoming) benchmark writeup from the section intro

* docs: add the Shannon vs XBOW/Aikido Photoview benchmark writeup

- Add docs/shannon-xbow-aikido-benchmark.md with methodology, per-model
  cost/coverage tables, and links to each model's report and SARIF
- Link the writeup from the README "Shannon in Action" section

* docs: link the benchmark announcement discussion from the README

* fix(readme): restore theme-aware banner, badge, and buttons

* feat!: trigger the Shannon 3.0 major release

---------

Co-authored-by: ezl-keygraph <ezhil@keygraph.io>

apps/cli/src/index.ts

@@ -18,14 +18,23 @@ import { setup } from './commands/setup.js';
 import { start } from './commands/start.js';
 import { status } from './commands/status.js';
 import { stop } from './commands/stop.js';
-import { crash, fail, failUsage } from './errors.js';
-import { availableCommands, isHelpableCommand, printCommandHelp, START_OPTIONS } from './help.js';
+import { hasExportedCredentials } from './env.js';
+import { crash, enableJsonErrors, fail, failUsage, failWith, jsonErrorsEnabled } from './errors.js';
+import { availableCommands, helpTopics, isHelpableCommand, printCommandHelp, START_OPTIONS } from './help.js';
+import { configFileExists } from './home.js';
 import { commandPrefix, getMode, isLocal, type Mode } from './mode.js';
 import { displaySplash } from './splash.js';
 import { closestMatch } from './suggest.js';
 import { stdoutIsTerminal } from './tty.js';
 import { getVersion, getVersionLine } from './version.js';
+import { resolveDefaultWorkspace } from './workspaces.js';
 
+/**
+ * Refuse to run as root or under sudo. The worker container's Linux UID remapping
+ * (docker.ts) stamps bind-mounted files with the invoking user's real uid/gid; under
+ * sudo that uid is 0, so the repo, workspace, and report files would come back
+ * owned by root instead of the person who ran the scan.
+ */
 function blockSudo(): void {
   const isSudo = !!process.env.SUDO_USER;
   const isRoot = process.geteuid?.() === 0;
@@ -37,15 +46,38 @@ function blockSudo(): void {
       : [];
 
   if (isSudo) {
-    fail('Shannon must not be run with sudo.', 'Re-run this command as your normal user.', ...linuxHints);
+    failWith(
+      'CLI_PRECONDITION_FAILED',
+      'Shannon must not be run with sudo.',
+      'Re-run this command as your normal user.',
+      ...linuxHints,
+    );
   }
-  fail(
+  failWith(
+    'CLI_PRECONDITION_FAILED',
     'Shannon must not be run as the root user.',
     'Switch to a regular user account and re-run this command.',
     ...linuxHints,
   );
 }
 
+/** Commands whose `--json` output contract extends to failures. */
+const JSON_CAPABLE_COMMANDS = new Set(['status', 'scans', 'version', '--version', '-v']);
+
+/**
+ * Raw-argv sniff for the JSON error latch, decided before any guard or parse so even
+ * a pre-dispatch failure honors it. Latches on `--json` or a malformed `--json=<value>`
+ * (which still fails as a parse error — inside the envelope). Any other command that
+ * receives `--json` keeps its normal unknown-option behavior.
+ */
+function wantsJsonErrors(argv: readonly string[]): boolean {
+  const command = argv[0];
+  if (command === undefined || !JSON_CAPABLE_COMMANDS.has(command)) {
+    return false;
+  }
+  return argv.slice(1).some((arg) => arg === '--json' || arg.startsWith('--json='));
+}
+
 /** Render `start`'s flags for the global help, from the same source as `start --help`. */
 function renderStartOptions(): string {
   const flagWidth = Math.max(...START_OPTIONS.map(([flag]) => flag.length));
@@ -60,12 +92,16 @@ function renderUsage(prefix: string, mode: Mode): string {
   const rows: ReadonlyArray<readonly [string, string]> = [
     ...(mode === 'local' ? [] : [[`${prefix} setup`, 'Configure credentials'] as const]),
     [`${prefix} start --url <url> --repo <path> [options]`, 'Start a pentest scan'],
-    [`${prefix} stop <workspace> [--yes]`, 'Stop one scan'],
+    [`${prefix} stop [<workspace>] [--yes]`, 'Stop one scan (default: the single running scan)'],
     [`${prefix} stop --all [--yes]`, 'Stop all scans (Temporal stays up)'],
     [`${prefix} reset`, 'Stop everything and wipe all Temporal data'],
-    [`${prefix} logs <workspace>`, "Show a scan's live log"],
-    [`${prefix} status <workspace> [--json]`, 'Live phase/agent progress of one scan'],
-    [`${prefix} scans [--json]`, 'List completed scans and their reports'],
+    [`${prefix} logs [<workspace>]`, "Show a scan's live log (default: running or most recent)"],
+    [`${prefix} logs [<workspace>] --agent <name>`, "Tail one agent's log; --list-agents to list them"],
+    [
+      `${prefix} status [<workspace>] [--json]`,
+      'Live phase/agent progress of one scan (default: running or most recent)',
+    ],
+    [`${prefix} scans [--json]`, 'List running and completed scans'],
     ...(mode === 'local' ? [[`${prefix} build [--no-cache]`, 'Build worker image'] as const] : []),
     [`${prefix} version [--json]`, 'Show version'],
     [`${prefix} help`, 'Show this help'],
@@ -75,13 +111,28 @@ function renderUsage(prefix: string, mode: Mode): string {
   return rows.map(([command, desc]) => `  ${command.padEnd(commandWidth)}   ${desc}`).join('\n');
 }
 
+/**
+ * A boxed "start your first scan" call to action, shown in help when no scans exist
+ * yet. Prefix-aware, so local mode renders `./shannon start …`.
+ */
+function renderFirstScanBox(prefix: string): string {
+  const command = `${prefix} start -u <url> -r <path>`;
+  const title = 'Start your first scan';
+  const padX = 3;
+  const inner = Math.max(command.length, title.length) + padX * 2;
+  const rule = (left: string, right: string): string => `  ${left}${'─'.repeat(inner)}${right}`;
+  const line = (text: string): string => `  │${' '.repeat(padX)}${text}${' '.repeat(inner - padX - text.length)}│`;
+  return [rule('╭', '╮'), line(title), line(''), line(command), rule('╰', '╯')].join('\n');
+}
+
 function showHelp(withSplash: boolean): void {
   const mode = getMode();
   const prefix = commandPrefix();
 
   const header = withSplash ? '' : '\nShannon — AI Pentester by Keygraph\n';
+  const firstScan = stdoutIsTerminal() ? `\n${renderFirstScanBox(prefix)}\n` : '';
 
-  console.log(`${header}
+  console.log(`${header}${firstScan}
 Usage:
 ${renderUsage(prefix, mode)}
 
@@ -101,6 +152,21 @@ Docs & source: https://github.com/KeygraphHQ/shannon
 `);
 }
 
+/**
+ * First-run guidance for a bare `npx @keygraph/shannon` invocation when neither a
+ * credentials file nor an exported shell credential exists. Walks the user to `setup`.
+ */
+function showSetupPrompt(): void {
+  const prefix = commandPrefix();
+  console.log(`
+Welcome to Shannon — AI Pentester by Keygraph
+
+No credentials configured yet. To get started, run:
+
+  ${prefix} setup
+`);
+}
+
 interface ParsedStartArgs {
   url: string;
   repo: string;
@@ -152,6 +218,32 @@ function parseStartArgs(argv: string[]): ParsedStartArgs {
   };
 }
 
+/**
+ * Resolve the workspace a viewing command (`logs`, `status`) acts on: the name the user
+ * gave, or an inferred default. An inferred choice is announced on stderr so it is never a
+ * silent guess; when nothing can be inferred, exit with usage guidance.
+ */
+function resolveViewingWorkspace(positional: string | undefined, usage: string): string {
+  if (positional) {
+    return positional;
+  }
+
+  const target = resolveDefaultWorkspace({ allowFinished: true });
+  if (target.kind === 'ok') {
+    // In JSON mode stderr is reserved for the single error envelope, so a successful
+    // inference stays silent — the JSON payload itself names the chosen workspace.
+    if (!jsonErrorsEnabled()) {
+      const which = target.running ? 'running scan' : 'most recent scan';
+      console.error(`No workspace given; using ${which} "${target.workspace}".`);
+    }
+    return target.workspace;
+  }
+  if (target.kind === 'ambiguous') {
+    failUsage('Multiple scans are running — specify which one:', `  ${target.running.join(', ')}`, '', usage);
+  }
+  failUsage('Workspace is required', usage);
+}
+
 // === Main Dispatch ===
 
 async function main(): Promise<void> {
@@ -163,24 +255,54 @@ async function main(): Promise<void> {
     throw err;
   });
 
+  if (wantsJsonErrors(process.argv.slice(2))) {
+    enableJsonErrors();
+  }
+
   blockSudo();
 
   const args = process.argv.slice(2);
   const command = args[0];
   const rest = args.slice(1);
 
-  if (command === undefined || command === 'help' || command === '--help' || command === '-h') {
+  if (command === undefined || command === '--help' || command === '-h') {
     const topic = rest[0];
     if (topic && isHelpableCommand(topic)) {
       printCommandHelp(topic);
     } else {
       const bare = command === undefined;
       if (bare && stdoutIsTerminal()) displaySplash(isLocal() ? undefined : getVersion());
-      showHelp(bare);
+      const needsSetup = bare && !isLocal() && !configFileExists() && !hasExportedCredentials();
+      if (needsSetup) {
+        showSetupPrompt();
+      } else {
+        showHelp(bare);
+      }
     }
     return;
   }
 
+  // An explicit `help <topic>` names a topic on purpose, so an unknown one is a usage
+  // error — unlike `--help <junk>`, where the junk is ignored and global help wins.
+  if (command === 'help') {
+    const topic = rest[0];
+    // A flag (`help --help`) is a help request, not a topic name.
+    if (topic === undefined || topic === 'help' || topic.startsWith('-')) {
+      showHelp(false);
+      return;
+    }
+    if (isHelpableCommand(topic)) {
+      printCommandHelp(topic);
+      return;
+    }
+    const suggestion = closestMatch(topic, helpTopics());
+    failUsage(
+      `Unknown help topic: ${topic}`,
+      ...(suggestion ? [`Did you mean '${suggestion}'?`] : []),
+      `Run '${commandPrefix()} help' to see available commands.`,
+    );
+  }
+
   // Reachable from any invocation: `-h`/`--help` anywhere wins over the rest of the line.
   if (isHelpableCommand(command) && (rest.includes('-h') || rest.includes('--help'))) {
     printCommandHelp(command);
@@ -210,20 +332,25 @@ async function main(): Promise<void> {
       break;
     }
     case 'logs': {
-      const { positionals } = parseArgs(rest, { maxPositionals: 1 });
-      const workspaceId = positionals[0];
-      if (!workspaceId) {
-        failUsage('Workspace ID is required', `Usage: ${commandPrefix()} logs <workspace>`);
-      }
-      logs(workspaceId);
+      const { flags, values, positionals } = parseArgs(rest, {
+        booleans: { listAgents: ['--list-agents'] },
+        values: { agent: ['--agent'] },
+        maxPositionals: 1,
+      });
+      const workspaceId = resolveViewingWorkspace(
+        positionals[0],
+        `Usage: ${commandPrefix()} logs [<workspace>] [--agent <name>] [--list-agents]`,
+      );
+      logs(workspaceId, {
+        ...(values.agent !== undefined && { agent: values.agent }),
+        ...(flags.listAgents && { listAgents: true }),
+      });
       break;
     }
     case 'status': {
       const { flags, positionals } = parseArgs(rest, { booleans: { json: ['--json'] }, maxPositionals: 1 });
-      const workspaceId = positionals[0];
-      if (!workspaceId) {
-        failUsage('Workspace is required', `Usage: ${commandPrefix()} status <workspace> [--json]`);
-      }
+      const usage = `Usage: ${commandPrefix()} status [<workspace>] [--json]`;
+      const workspaceId = resolveViewingWorkspace(positionals[0], usage);
       await status(workspaceId, { json: !!flags.json });
       break;
     }