create-quiver 0.10.0 → 0.12.0

package/src/create-quiver/index.js

@@ -3,15 +3,27 @@ const os = require('os');
 const path = require('path');
 const { execFileSync } = require('child_process');
 const { checkHandoff, scaffoldHandoff } = require('./lib/handoff');
-const { collectDoctorReport } = require('./lib/doctor');
-const { runDoctor: runAiDoctor, runExecuteSlice: runAiExecuteSlice, runOnboard, runPlan: runAiPlan, runPr: runAiPr } = require('./commands/ai');
+const {
+  applyDoctorFixPlan,
+  buildDoctorFixPlan,
+  collectDoctorReport,
+  formatDoctorFixPlan,
+} = require('./lib/doctor');
+const { runAgent: runAiAgent, runApprovalStatus: runAiApprovalStatus, runApprove: runAiApprove, runDoctor: runAiDoctor, runExecutePlan: runAiExecutePlan, runExecuteSlice: runAiExecuteSlice, runOnboard, runPlan: runAiPlan, runPrepareContext: runAiPrepareContext, runPr: runAiPr, runPromptSlice: runAiPromptSlice, runReviewPlan: runAiReviewPlan } = require('./commands/ai');
+const { runDemo } = require('./commands/demo');
+const { runPrepare } = require('./commands/prepare');
+const { runEvidence } = require('./commands/evidence');
+const { runFlow } = require('./commands/flow');
 const { runGraph } = require('./commands/graph');
 const { runNext } = require('./commands/next');
 const { runPlan } = require('./commands/plan');
+const { runCreateSpec } = require('./commands/spec');
 const { buildInitLayout, formatInitLayoutPlan } = require('./lib/init-layout');
-const { initializeProjectDocs, installSelfAsDevDep } = require('./lib/init-docs');
+const { initializeProjectDocs, installSelfAsDevDep, refreshAiContextDoc } = require('./lib/init-docs');
 const { checkPrReadiness, checkScope, checkSliceReadiness } = require('./lib/readiness');
 const { cleanupSlice, refreshActiveSlicesBoard, startSlice } = require('./lib/lifecycle');
+const { buildSpecStatus, closeSpecWorktree, formatSpecCloseResult, formatSpecStartResult, formatSpecStatus, startSpecWorktree } = require('./lib/spec-worktrees');
+const { getContextPathExclusionReason } = require('./lib/ai/safety');
 const { relativePosixPath, resolveTargetRoot } = require('./lib/paths');
 const {
   CURRENT_SCAN_RELATIVE_PATH,
@@ -35,17 +47,74 @@ function formatError(message) {
   return `create-quiver: ${message}`;
 }
 
+const SUPPORTED_COMMAND_MODES = new Set([
+  'init',
+  'flow',
+  'plan',
+  'graph',
+  'next',
+  'doctor',
+  'prepare',
+  'analyze',
+  'migrate',
+  'start-slice',
+  'check-slice',
+  'check-pr',
+  'check-handoff',
+  'new-handoff',
+  'cleanup-slice',
+  'check-scope',
+  'refresh-active-slices',
+  'spec',
+  'evidence',
+  'demo',
+  'ai',
+]);
+
+const SUPPORTED_AI_COMMANDS = new Set([
+  'agent',
+  'approve',
+  'approval-status',
+  'approvals',
+  'doctor',
+  'execute-plan',
+  'execute-slice',
+  'executor-prompt',
+  'onboard',
+  'plan',
+  'prepare-context',
+  'pr',
+  'prompt-slice',
+  'review-plan',
+]);
+
+const SUPPORTED_SPEC_COMMANDS = new Set(['close', 'create', 'start', 'status']);
+const SUPPORTED_DEMO_COMMANDS = new Set(['create']);
+
+function unsupportedCommandMessage(commandName) {
+  return [
+    `unsupported command: ${commandName}`,
+    'Run: npx create-quiver --help',
+    `If you meant to initialize a project, use: npx create-quiver init --name "${commandName}"`,
+    'If this command exists in newer docs, update create-quiver and rerun the command.',
+  ].join('\n');
+}
+
 function printUsage() {
   console.log(`Usage:
   npx create-quiver [options]
   npx create-quiver init [options]
   npx create-quiver analyze [options]
+  npx create-quiver flow [options]
   npx create-quiver plan [options]
   npx create-quiver ai <task> [options]
+  npx create-quiver ai agent <set|list|show> [role] [options]
+  npx create-quiver ai prepare-context [options]
   npx create-quiver graph [options]
   npx create-quiver next [options]
   npx create-quiver migrate [options]
   npx create-quiver doctor [options]
+  npx create-quiver prepare [options]
   npx create-quiver start-slice [options] <slice.json>
   npx create-quiver check-slice [options] <slice.json>
   npx create-quiver check-pr <slice.json>
@@ -54,6 +123,12 @@ function printUsage() {
   npx create-quiver cleanup-slice [options] <slice.json>
   npx create-quiver check-scope [options] <slice.json>
   npx create-quiver refresh-active-slices
+  npx create-quiver spec create [options]
+  npx create-quiver spec start <spec-dir>
+  npx create-quiver spec status <spec-dir>
+  npx create-quiver spec close <spec-dir>
+  npx create-quiver evidence run [options] -- <command>
+  npx create-quiver demo create spec-viewer [options]
 
 Options:
   -n, --name <project-name>   Project name to generate
@@ -63,15 +138,33 @@ Options:
       --show-conflicts        Show shared file paths in graph output
       --level <n>             Restrict graph output to one level
       --json                  Emit machine-readable JSON
+      --include-completed     Include completed slices in plan, graph, or next history output
       --only-ready            Show only slices with no pending dependencies
       --all-ready             List every ready slice returned by next
       --auto-start            Prompt for confirmation and run start-slice on next
+      --local                 For check-slice, run structural validation without remote/base checks
       --unicode               Prefer Unicode output when supported
       --minimal               Plan or run the minimal init profile
       --full                  Plan or run the full compatibility init profile
       --legacy-scripts        Include legacy Bash wrappers in init profile
       --include-templates     Export packaged templates in init profile
-      --dry-run               Preview init or AI work without executing writes/providers
+      --dry-run               Preview init, prepare, spec create, demo, or AI work without executing writes/providers
+      --fix                   For doctor, apply safe non-destructive repairs
+      --execute               For ai execute-plan, run the planned slices instead of printing commands
+      --create                For ai pr, create the PR after preflight instead of printing the plan only
+      --commit                For ai execute-slice, commit validated slice changes after provider, scope, and tests pass
+      --allow-dirty           For ai execute-slice, allow pre-existing dirty files and ignore them for scope diff
+      --mode <name>           Execution mode for ai execute-plan (auto, manual, delegated)
+      --provider <name>       Provider CLI to preflight for prepare or AI commands
+      --model <label>         Free-form model label for AI agent profiles
+      --version <n>           Draft version to approve for AI planner phases
+      --ssh-host-alias <name> SSH host alias to validate for prepare or AI commands
+      --identity-file <path>  SSH identity file to validate for prepare or AI commands
+      --remote <name>         Git remote name for check-slice or AI PR checks
+      --base <branch>         Base branch for check-slice, ai pr, or spec close (default: main)
+      --output <file>         Output file for evidence run
+      --max-output <n>        Maximum stdout/stderr chars per evidence section
+      --title <text>          Override PR title for ai pr create
   -y, --yes                   Skip prompts and use the provided inputs
   -h, --help                  Show this help message
 
@@ -80,13 +173,28 @@ Examples:
   npx create-quiver init --name "My Project" --dry-run
   npx create-quiver --name "My Project"
   npx create-quiver --name "My Project" --dir ./my-project
+  cd ./my-project && npx create-quiver flow
   cd ./my-project && npx create-quiver analyze
   cd ./my-project && npx create-quiver plan --json
   cd ./my-project && npx create-quiver ai onboard --dry-run
+  cd ./my-project && npx create-quiver ai prepare-context --dry-run
+  cd ./my-project && npx create-quiver ai agent set planner --provider codex --model gpt-5.5
+  cd ./my-project && npx create-quiver ai agent list
   cd ./my-project && npx create-quiver ai plan --phase acceptance --input requirements.md --dry-run
+  cd ./my-project && npx create-quiver ai approve --phase acceptance --input acceptance.md
+  cd ./my-project && npx create-quiver ai plan --phase technical-plan --dry-run
+  cd ./my-project && npx create-quiver ai review-plan --dry-run
+  cd ./my-project && npx create-quiver ai approve --phase technical-plan --version 1
+  cd ./my-project && npx create-quiver spec create --dry-run
+  cd ./my-project && npx create-quiver ai approvals
+  cd ./my-project && npx create-quiver ai prompt-slice --slice specs/my-project/slices/slice-01/slice.json --dry-run
   cd ./my-project && npx create-quiver ai execute-slice --slice specs/my-project/slices/slice-01/slice.json --dry-run
+  cd ./my-project && npx create-quiver ai execute-slice --slice specs/my-project/slices/slice-01/slice.json --commit
+  cd ./my-project && npx create-quiver ai execute-plan --dry-run --commit
   cd ./my-project && npx create-quiver ai doctor --dry-run --ssh-host-alias github-work --identity-file ~/.ssh/github-work
   cd ./my-project && npx create-quiver ai pr --dry-run --ssh-host-alias github-work --identity-file ~/.ssh/github-work
+  cd ./my-project && npx create-quiver ai pr --create --input specs/my-project/pr.md --ssh-host-alias github-work --identity-file ~/.ssh/github-work
+  cd ./my-project && npx create-quiver prepare --dry-run --provider codex --ssh-host-alias github-work --identity-file ~/.ssh/github-work
   cd ./my-project && npx create-quiver graph --show-conflicts
   cd ./my-project && npx create-quiver graph --format mermaid
   cd ./my-project && npx create-quiver graph --format dot
@@ -103,6 +211,11 @@ Examples:
   cd ./my-project && npx create-quiver cleanup-slice specs/my-project/slices/slice-01/slice.json
   cd ./my-project && npx create-quiver check-scope specs/my-project/slices/slice-01/slice.json
   cd ./my-project && npx create-quiver refresh-active-slices
+  cd ./my-project && npx create-quiver spec start specs/my-project
+  cd ./my-project && npx create-quiver spec status specs/my-project
+  cd ./my-project && npx create-quiver spec close specs/my-project --dry-run
+  cd ./my-project && npx create-quiver evidence run -- npm test
+  cd ./my-project && npx create-quiver demo create spec-viewer --dry-run
   node bin/create-quiver.js doctor --dir ./my-project
 `);
 }
@@ -114,15 +227,19 @@ function parseArgs(argv) {
     explicitInit: false,
     mode: 'init',
     allowDraft: false,
+    checkSliceLocal: false,
     closeBaseline: false,
     discard: false,
+    doctorFix: false,
     dryRun: false,
     gate: 'execution',
     projectName: '',
     targetDir: '.',
+    targetDirExplicit: false,
     strict: false,
     strictOverlap: false,
     json: false,
+    includeCompleted: false,
     onlyReady: false,
     allReady: false,
     autoStart: false,
@@ -132,13 +249,28 @@ function parseArgs(argv) {
     level: null,
     unicode: false,
     aiCommand: '',
+    aiAgentCommand: '',
+    aiAgentRole: '',
     aiPhase: 'acceptance',
     aiProvider: 'codex',
+    aiProviderExplicit: false,
+    aiModel: '',
+    aiLabel: '',
+    aiVersion: '',
+    prepareProvider: '',
     aiRole: '',
     aiContext: '',
     aiInput: '',
     aiSlice: '',
     aiTimeout: null,
+    aiCommit: false,
+    aiAllowDirty: false,
+    aiExecute: false,
+    aiExecutionMode: 'auto',
+    aiCreate: false,
+    aiBaseBranch: 'main',
+    baseBranchExplicit: false,
+    aiTitle: '',
     aiSshHostAlias: '',
     aiIdentityFile: '',
     aiRemote: 'origin',
@@ -146,14 +278,30 @@ function parseArgs(argv) {
     initIncludeTemplates: false,
     initLegacyScripts: false,
     initMinimal: false,
+    specCommand: '',
+    demoCommand: '',
+    demoName: '',
+    evidenceCommand: '',
+    evidenceArgs: [],
+    evidenceOutput: '',
+    evidenceMaxOutput: null,
   };
 
   const args = [...argv];
-  const commandModes = new Set(['init', 'plan', 'graph', 'next', 'doctor', 'analyze', 'migrate', 'start-slice', 'check-slice', 'check-pr', 'check-handoff', 'new-handoff', 'cleanup-slice', 'check-scope', 'refresh-active-slices', 'ai']);
-  if (commandModes.has(args[0])) {
+  if (SUPPORTED_COMMAND_MODES.has(args[0])) {
     result.mode = args[0];
     result.explicitInit = args[0] === 'init';
     args.shift();
+    if (result.mode === 'spec') {
+      result.specCommand = args.shift() || '';
+    }
+    if (result.mode === 'evidence') {
+      result.evidenceCommand = args.shift() || '';
+    }
+    if (result.mode === 'demo') {
+      result.demoCommand = args.shift() || '';
+      result.demoName = args.shift() || '';
+    }
   } else if (args[0] === '--analyze') {
     result.mode = 'analyze';
     args.shift();
@@ -169,6 +317,8 @@ function parseArgs(argv) {
   } else if (args[0] === '--new-handoff') {
     result.mode = 'new-handoff';
     args.shift();
+  } else if (args[0] && !args[0].startsWith('-')) {
+    throw new Error(formatError(unsupportedCommandMessage(args[0])));
   }
 
   const positional = [];
@@ -176,6 +326,11 @@ function parseArgs(argv) {
   for (let index = 0; index < args.length; index += 1) {
     const arg = args[index];
 
+    if (arg === '--') {
+      result.evidenceArgs = args.slice(index + 1);
+      break;
+    }
+
     if (arg === '-h' || arg === '--help') {
       result.help = true;
       continue;
@@ -216,6 +371,11 @@ function parseArgs(argv) {
       continue;
     }
 
+    if (arg === '--local') {
+      result.checkSliceLocal = true;
+      continue;
+    }
+
     if (arg === '--close-baseline') {
       result.closeBaseline = true;
       continue;
@@ -226,11 +386,45 @@ function parseArgs(argv) {
       continue;
     }
 
+    if (arg === '--fix') {
+      result.doctorFix = true;
+      continue;
+    }
+
     if (arg === '--dry-run') {
       result.dryRun = true;
       continue;
     }
 
+    if (arg === '--commit') {
+      result.aiCommit = true;
+      continue;
+    }
+
+    if (arg === '--execute') {
+      result.aiExecute = true;
+      continue;
+    }
+
+    if (arg === '--create') {
+      result.aiCreate = true;
+      continue;
+    }
+
+    if (arg === '--mode') {
+      const value = args[++index];
+      if (!value) {
+        throw new Error(formatError('missing value for --mode'));
+      }
+      result.aiExecutionMode = value;
+      continue;
+    }
+
+    if (arg === '--allow-dirty') {
+      result.aiAllowDirty = true;
+      continue;
+    }
+
     if (arg === '--minimal') {
       result.initMinimal = true;
       continue;
@@ -266,6 +460,11 @@ function parseArgs(argv) {
       continue;
     }
 
+    if (arg === '--include-completed') {
+      result.includeCompleted = true;
+      continue;
+    }
+
     if (arg === '--show-conflicts') {
       result.showConflicts = true;
       continue;
@@ -319,6 +518,35 @@ function parseArgs(argv) {
         throw new Error(formatError('missing value for --provider'));
       }
       result.aiProvider = value;
+      result.prepareProvider = value;
+      result.aiProviderExplicit = true;
+      continue;
+    }
+
+    if (arg === '--model') {
+      const value = args[++index];
+      if (!value) {
+        throw new Error(formatError('missing value for --model'));
+      }
+      result.aiModel = value;
+      continue;
+    }
+
+    if (arg === '--label') {
+      const value = args[++index];
+      if (!value) {
+        throw new Error(formatError('missing value for --label'));
+      }
+      result.aiLabel = value;
+      continue;
+    }
+
+    if (arg === '--version') {
+      const value = args[++index];
+      if (!value) {
+        throw new Error(formatError('missing value for --version'));
+      }
+      result.aiVersion = value;
       continue;
     }
 
@@ -398,6 +626,47 @@ function parseArgs(argv) {
       continue;
     }
 
+    if (arg === '--base') {
+      const value = args[++index];
+      if (!value) {
+        throw new Error(formatError('missing value for --base'));
+      }
+      result.aiBaseBranch = value;
+      result.baseBranchExplicit = true;
+      continue;
+    }
+
+    if (arg === '--output') {
+      const value = args[++index];
+      if (!value) {
+        throw new Error(formatError('missing value for --output'));
+      }
+      result.evidenceOutput = value;
+      continue;
+    }
+
+    if (arg === '--max-output') {
+      const value = args[++index];
+      if (typeof value === 'undefined') {
+        throw new Error(formatError('missing value for --max-output'));
+      }
+      const parsed = Number.parseInt(value, 10);
+      if (!Number.isInteger(parsed) || parsed <= 0) {
+        throw new Error(formatError('invalid value for --max-output'));
+      }
+      result.evidenceMaxOutput = parsed;
+      continue;
+    }
+
+    if (arg === '--title') {
+      const value = args[++index];
+      if (!value) {
+        throw new Error(formatError('missing value for --title'));
+      }
+      result.aiTitle = value;
+      continue;
+    }
+
     if (arg === '--phase') {
       const value = args[++index];
       if (!value) {
@@ -440,6 +709,7 @@ function parseArgs(argv) {
         throw new Error(formatError('missing value for --dir'));
       }
       result.targetDir = value;
+      result.targetDirExplicit = true;
       continue;
     }
 
@@ -462,17 +732,78 @@ function parseArgs(argv) {
     if (positional.length > 0) {
       throw new Error(formatError('plan does not accept positional arguments; use --spec <slug>'));
     }
+  } else if (result.mode === 'flow') {
+    if (positional.length > 0) {
+      throw new Error(formatError('flow does not accept positional arguments'));
+    }
   } else if (result.mode === 'ai') {
     if (!result.aiCommand && positional.length > 0) {
       result.aiCommand = positional.shift();
     }
+    if (result.aiCommand === 'agent') {
+      if (!result.aiAgentCommand && positional.length > 0) {
+        result.aiAgentCommand = positional.shift();
+      }
+      if (!result.aiAgentRole && positional.length > 0) {
+        result.aiAgentRole = positional.shift();
+      }
+    }
     if (positional.length > 0) {
       throw new Error(formatError('ai does not accept extra positional arguments'));
     }
+  } else if (result.mode === 'prepare') {
+    if (positional.length > 0) {
+      throw new Error(formatError('prepare does not accept positional arguments'));
+    }
   } else if (result.mode === 'refresh-active-slices') {
     if (positional.length > 0) {
       throw new Error(formatError('refresh-active-slices does not accept positional arguments'));
     }
+  } else if (result.mode === 'spec') {
+    if (!result.specCommand && positional.length > 0) {
+      result.specCommand = positional.shift();
+    }
+    if (!result.specCommand) {
+      throw new Error(formatError('missing spec subcommand. Use: npx create-quiver spec <create|start|status|close>'));
+    }
+    if (result.specCommand !== 'create' && positional.length > 0) {
+      result.targetDir = positional.shift();
+    }
+    if (result.specCommand === 'create' && positional.length > 0) {
+      throw new Error(formatError('spec create does not accept positional arguments; use --input <file> or --spec <slug>'));
+    }
+  } else if (result.mode === 'evidence') {
+    if (!result.evidenceCommand && positional.length > 0) {
+      result.evidenceCommand = positional.shift();
+    }
+    if (!result.evidenceCommand) {
+      throw new Error(formatError('missing evidence subcommand. Use: npx create-quiver evidence run -- <command>'));
+    }
+    if (result.evidenceCommand !== 'run') {
+      throw new Error(formatError(`unsupported evidence subcommand: ${result.evidenceCommand}. Supported tasks: run`));
+    }
+    if (positional.length > 0) {
+      throw new Error(formatError('evidence run does not accept positional arguments before --'));
+    }
+  } else if (result.mode === 'demo') {
+    if (!result.demoCommand && positional.length > 0) {
+      result.demoCommand = positional.shift();
+    }
+    if (!result.demoName && positional.length > 0) {
+      result.demoName = positional.shift();
+    }
+    if (!result.demoCommand) {
+      throw new Error(formatError('missing demo subcommand. Use: npx create-quiver demo create spec-viewer'));
+    }
+    if (!SUPPORTED_DEMO_COMMANDS.has(result.demoCommand)) {
+      throw new Error(formatError(`unsupported demo subcommand: ${result.demoCommand}. Supported tasks: create`));
+    }
+    if (result.demoName !== 'spec-viewer') {
+      throw new Error(formatError(`unsupported demo: ${result.demoName || '(missing)'}. Supported demos: spec-viewer`));
+    }
+    if (positional.length > 0) {
+      throw new Error(formatError('demo create spec-viewer does not accept positional target paths; use --dir <target-dir>'));
+    }
   } else {
     if (positional.length > 0) {
       result.targetDir = positional.shift();
@@ -698,6 +1029,43 @@ function escapeMarkdownCell(value) {
   return String(value).replace(/\|/g, '\\|');
 }
 
+function summarizeSkippedPaths(scan) {
+  const details = Array.isArray(scan.skipped_path_details) && scan.skipped_path_details.length > 0
+    ? scan.skipped_path_details
+    : (Array.isArray(scan.skipped_paths) ? scan.skipped_paths.map((item) => ({ reason: 'excluded path', path: item })) : []);
+  const counts = new Map();
+  const dependencySegments = new Set(['node_modules', '.pnpm-store', '.npm', '.yarn']);
+  const outputSegments = new Set(['dist', 'build', 'coverage', 'out', 'tmp', 'temp', 'cache', '.cache', '.turbo', '.next', '.nuxt', '.parcel-cache', 'generated', 'gen', 'artifacts', 'reports', 'vendor', 'target']);
+
+  for (const item of details) {
+    const reason = item.reason || 'excluded path';
+    let label = reason;
+    if (reason === 'env-file') {
+      label = 'env files';
+    } else if (reason === 'git-metadata') {
+      label = 'git metadata';
+    } else if (reason === 'hidden-directory') {
+      label = 'hidden directories';
+    } else if (reason.startsWith('secret-file:')) {
+      label = 'secret files';
+    } else if (reason.startsWith('unsafe-segment:')) {
+      const segment = reason.slice('unsafe-segment:'.length);
+      if (segment === '.quiver') {
+        label = 'local AI state';
+      } else if (dependencySegments.has(segment)) {
+        label = 'dependency folders';
+      } else if (outputSegments.has(segment)) {
+        label = 'generated/output/cache folders';
+      } else {
+        label = segment;
+      }
+    }
+    counts.set(label, (counts.get(label) || 0) + 1);
+  }
+
+  return Array.from(counts.entries()).map(([reason, count]) => ({ reason, count }));
+}
+
 function collectPackageManagers(projectRoot) {
   const packageManagerField = readJsonIfExists(path.join(projectRoot, 'package.json'))?.packageManager;
 
@@ -725,6 +1093,7 @@ function collectPackageManagers(projectRoot) {
 function collectProjectFiles(projectRoot, maxDepth = 2) {
   const files = [];
   const skippedPaths = [];
+  const skippedPathDetails = [];
   const ignoredDirs = new Set([
     '.git',
     'node_modules',
@@ -741,6 +1110,12 @@ function collectProjectFiles(projectRoot, maxDepth = 2) {
   ]);
   const allowedHiddenDirs = new Set(['.github', '.vscode', '.devcontainer']);
 
+  function skipPath(relativePath, reason) {
+    const normalized = relativePath.split(path.sep).join('/');
+    skippedPaths.push(normalized);
+    skippedPathDetails.push({ path: normalized, reason });
+  }
+
   function walk(currentDir, depth, relativeDir = '') {
     const entries = fs.readdirSync(currentDir, { withFileTypes: true });
 
@@ -750,12 +1125,18 @@ function collectProjectFiles(projectRoot, maxDepth = 2) {
 
       if (entry.isDirectory()) {
         if (ignoredDirs.has(entry.name)) {
-          skippedPaths.push(entryRelativePath);
+          skipPath(entryRelativePath, `unsafe-segment:${entry.name}`);
+          continue;
+        }
+
+        const directoryReason = getContextPathExclusionReason(entryRelativePath);
+        if (directoryReason) {
+          skipPath(entryRelativePath, directoryReason);
           continue;
         }
 
         if (entry.name.startsWith('.') && !allowedHiddenDirs.has(entry.name)) {
-          skippedPaths.push(entryRelativePath);
+          skipPath(entryRelativePath, 'hidden-directory');
           continue;
         }
 
@@ -766,13 +1147,19 @@ function collectProjectFiles(projectRoot, maxDepth = 2) {
         continue;
       }
 
+      const fileReason = getContextPathExclusionReason(entryRelativePath);
+      if (fileReason) {
+        skipPath(entryRelativePath, fileReason);
+        continue;
+      }
+
       files.push(entryRelativePath);
     }
   }
 
   walk(projectRoot, 0);
 
-  return { files, skippedPaths };
+  return { files, skipped_path_details: skippedPathDetails, skippedPaths };
 }
 
 function collectRootEntries(projectRoot) {
@@ -820,6 +1207,7 @@ function collectLanguageSignals(files) {
   }
 
   const languages = [];
+  const seenLanguages = new Set();
   const extToLanguage = new Map([
     ['.ts', 'typescript'],
     ['.tsx', 'typescript'],
@@ -845,14 +1233,90 @@ function collectLanguageSignals(files) {
   ]);
 
   for (const [ext, language] of extToLanguage.entries()) {
-    if (extensions.has(ext)) {
+    if (extensions.has(ext) && !seenLanguages.has(language)) {
       languages.push(language);
+      seenLanguages.add(language);
     }
   }
 
   return languages;
 }
 
+function parseCreateQuiverScriptCommand(command) {
+  const normalized = String(command || '').trim();
+  const match = normalized.match(/^npx\s+create-quiver(?:@[^\s]+)?\s+(.+)$/);
+  if (!match) {
+    return null;
+  }
+
+  const tokens = match[1].split(/\s+/).filter(Boolean);
+  if (tokens.length === 0) {
+    return null;
+  }
+
+  return {
+    commandName: tokens[0],
+    subcommand: tokens[1] || '',
+  };
+}
+
+function findUnsupportedCreateQuiverScripts(scripts = {}) {
+  const unsupported = [];
+
+  for (const [scriptName, command] of Object.entries(scripts)) {
+    const parsed = parseCreateQuiverScriptCommand(command);
+    if (!parsed) {
+      continue;
+    }
+
+    if (!SUPPORTED_COMMAND_MODES.has(parsed.commandName)) {
+      unsupported.push({
+        command,
+        reason: `unsupported command "${parsed.commandName}"`,
+        scriptName,
+      });
+      continue;
+    }
+
+    if (parsed.commandName === 'ai' && !SUPPORTED_AI_COMMANDS.has(parsed.subcommand)) {
+      unsupported.push({
+        command,
+        reason: `unsupported ai subcommand "${parsed.subcommand || '(missing)'}"`,
+        scriptName,
+      });
+      continue;
+    }
+
+    if (parsed.commandName === 'spec' && !SUPPORTED_SPEC_COMMANDS.has(parsed.subcommand)) {
+      unsupported.push({
+        command,
+        reason: `unsupported spec subcommand "${parsed.subcommand || '(missing)'}"`,
+        scriptName,
+      });
+      continue;
+    }
+
+    if (parsed.commandName === 'demo' && !SUPPORTED_DEMO_COMMANDS.has(parsed.subcommand)) {
+      unsupported.push({
+        command,
+        reason: `unsupported demo subcommand "${parsed.subcommand || '(missing)'}"`,
+        scriptName,
+      });
+    }
+  }
+
+  return unsupported;
+}
+
+function detectNodeProject(files, rootEntries, packageJson, languages) {
+  const hasPackageJson = Boolean(packageJson);
+  const hasJavaScriptSignals = languages.some((language) => language === 'javascript' || language === 'typescript');
+  const hasSourceDirectories = detectSourceDirectories(rootEntries).length > 0;
+  const hasSourceFiles = files.some((file) => /\.(?:c|m)?jsx?$/i.test(file) || /\.(?:c|m)?tsx?$/i.test(file));
+
+  return hasJavaScriptSignals && (hasPackageJson || hasSourceDirectories || hasSourceFiles);
+}
+
 function collectWorkspaces(packageJson) {
   if (!packageJson) {
     return [];
@@ -982,6 +1446,11 @@ function detectFrameworks(projectRoot, files, rootEntries, packageJson) {
     evidence.push({ framework: 'react', signals: ['react', 'typescript files'] });
   }
 
+  if (frameworks.length === 0 && detectNodeProject(files, rootEntries, packageJson, languages)) {
+    frameworks.push('node');
+    evidence.push({ framework: 'node', signals: ['package.json', 'javascript or typescript source files'] });
+  }
+
   const primary = frameworks[0] || 'unknown';
 
   return {
@@ -1076,7 +1545,7 @@ function detectRisks(projectRoot, scan) {
 function buildProjectScan(projectRoot) {
   const packageJson = readJsonIfExists(path.join(projectRoot, 'package.json'));
   const rootEntries = collectRootEntries(projectRoot);
-  const { files, skippedPaths } = collectProjectFiles(projectRoot);
+  const { files, skippedPaths, skipped_path_details } = collectProjectFiles(projectRoot);
   const topLevelDirectories = rootEntries.filter((entry) => entry.type === 'directory' && !entry.name.startsWith('.')).map((entry) => entry.name);
   const sourceDirectories = detectSourceDirectories(rootEntries);
   const configFiles = detectConfigFiles(rootEntries);
@@ -1134,6 +1603,7 @@ function buildProjectScan(projectRoot) {
     },
     risks: [],
     skipped_paths: skippedPaths,
+    skipped_path_details,
   };
 
   scan.risks = detectRisks(projectRoot, scan);
@@ -1250,7 +1720,7 @@ function renderProjectMap(scan) {
   }
 
   const relevantScripts = Object.entries(scan.commands.scripts)
-    .filter(([name]) => /(^|:)(analyze|doctor|migrate|test|build|lint|dev|start|check)(:|$)|analyze|doctor|migrate|test|build|lint|dev|start|check/i.test(name))
+    .filter(([name]) => /(^|:)(analyze|doctor|migrate|validate|test|build|lint|dev|start|check)(:|$)|analyze|doctor|migrate|validate|test|build|lint|dev|start|check/i.test(name))
     .slice(0, 12);
 
   if (relevantScripts.length > 0) {
@@ -1310,9 +1780,10 @@ function renderProjectMap(scan) {
 
   lines.push('');
   lines.push('## Skipped Paths');
-  if (scan.skipped_paths.length > 0) {
-    for (const skippedPath of scan.skipped_paths) {
-      lines.push(`- ${skippedPath}`);
+  const skippedSummaries = summarizeSkippedPaths(scan);
+  if (skippedSummaries.length > 0) {
+    for (const skippedPath of skippedSummaries) {
+      lines.push(`- ${skippedPath.reason}: ${skippedPath.count}`);
     }
   } else {
     lines.push('- None');
@@ -1320,10 +1791,8 @@ function renderProjectMap(scan) {
 
   lines.push('');
   lines.push('## Do Not Read First');
-  if (scan.skipped_paths.length > 0) {
-    for (const skippedPath of scan.skipped_paths) {
-      lines.push(`- ${skippedPath}`);
-    }
+  if (skippedSummaries.length > 0) {
+    lines.push('- Hidden, generated, secret, and cache paths are excluded from the analysis scan.');
   } else {
     lines.push('- None detected, but still prioritize docs and config files before source trees.');
   }
@@ -1351,11 +1820,13 @@ function runAnalyze(targetDir) {
 
   const scan = buildProjectScan(projectRoot);
   const artifacts = writeProjectScanArtifacts(projectRoot, scan);
+  const aiContextPath = refreshAiContextDoc(projectRoot, scan);
   updateStateForAnalyze(projectRoot, CLI_VERSION);
 
   console.log(`Project analysis completed for ${projectRoot}`);
   console.log(`Wrote ${relativePosixPath(projectRoot, artifacts.jsonPath)}`);
   console.log(`Wrote ${relativePosixPath(projectRoot, artifacts.mdPath)}`);
+  console.log(`Wrote ${relativePosixPath(projectRoot, aiContextPath)}`);
   console.log(`Detected primary stack: ${scan.stack.primary}`);
   console.log(`Detected package manager: ${scan.project.package_manager}`);
 }
@@ -1410,7 +1881,7 @@ function runMigrate(targetDir, options = {}) {
   }
 }
 
-function runDoctor(targetDir) {
+function runDoctor(targetDir, options = {}) {
   const projectRoot = resolveTargetRoot(process.cwd(), targetDir);
 
   if (!fs.existsSync(projectRoot)) {
@@ -1421,6 +1892,17 @@ function runDoctor(targetDir) {
     throw new Error(formatError('doctor requires a project previously initialized by Quiver.\nRun init first: npx create-quiver --name "Project Name"'));
   }
 
+  const fixPlan = buildDoctorFixPlan(projectRoot);
+  if (options.fix) {
+    if (options.dryRun) {
+      console.log(formatDoctorFixPlan(fixPlan, { dryRun: true }));
+      return;
+    }
+
+    applyDoctorFixPlan(projectRoot, fixPlan);
+    console.log(formatDoctorFixPlan(fixPlan));
+  }
+
   const doctorReport = collectDoctorReport(projectRoot);
   const specSlugs = doctorReport.specSlugs;
   const specRequiredFiles = specSlugs.flatMap((projectSlug) => [
@@ -1475,12 +1957,18 @@ function runDoctor(targetDir) {
   const missingNodeNativeScripts = ['quiver:migrate', 'quiver:analyze', 'quiver:doctor']
     .filter((name) => typeof pkg.scripts?.[name] !== 'string');
   const missingAiScripts = [
+    'quiver:ai:agent',
     'quiver:ai:onboard',
     'quiver:ai:plan',
+    'quiver:ai:review-plan',
+    'quiver:ai:approve',
+    'quiver:ai:prompt-slice',
     'quiver:ai:execute-slice',
+    'quiver:ai:execute-plan',
     'quiver:ai:pr',
     'quiver:ai:doctor',
   ].filter((name) => typeof pkg.scripts?.[name] !== 'string');
+  const unsupportedCreateQuiverScripts = findUnsupportedCreateQuiverScripts(pkg.scripts || {});
   const hasScanArtifacts = hasProjectScanArtifact(projectRoot)
     && fs.existsSync(path.join(projectRoot, PROJECT_MAP_RELATIVE_PATH));
   const quiverState = readState(projectRoot);
@@ -1523,6 +2011,9 @@ function runDoctor(targetDir) {
   if (legacyOnlyScripts.length > 0) {
     console.log(`- Warning: legacy Bash workflow scripts detected for ${legacyOnlyScripts.join(', ')}. Run npx create-quiver migrate to add quiver:* npm scripts.`);
   }
+  for (const script of unsupportedCreateQuiverScripts) {
+    console.log(`- Warning: package.json script ${script.scriptName} targets ${script.reason}: \`${script.command}\`. Update create-quiver or regenerate scripts with npx create-quiver migrate.`);
+  }
   for (const warning of softWarnings) {
     console.log(`- Warning: ${warning}`);
   }
@@ -1540,7 +2031,7 @@ function runDoctor(targetDir) {
     console.log(`- Validate a slice: npx create-quiver check-slice specs/${projectSlug}/slices/<slice-id>/slice.json`);
     console.log(`- Validate the PR gate: npx create-quiver check-pr specs/${projectSlug}/slices/<slice-id>/slice.json`);
   } else {
-    console.log('- Create real specs and slices only after acceptance criteria and the technical plan are approved.');
+    console.log('- Create real specs and slices only after acceptance criteria are approved and the technical plan is reviewed and approved.');
   }
 }
 
@@ -1550,7 +2041,7 @@ function printInitNextSteps(targetDir, projectName) {
   console.log(`- Review AGENTS.md, then ${path.join(targetDir, 'docs', 'AI_ONBOARDING_PROMPT.md')}`);
   console.log(`- Review ${path.join(targetDir, 'docs', 'WORKFLOW.md')}`);
   console.log('- Analyze the project with npx create-quiver analyze');
-  console.log('- Create real specs and slices after acceptance criteria and the technical plan are approved.');
+  console.log('- Create real specs and slices after acceptance criteria are approved and the technical plan is reviewed and approved.');
 }
 
 async function run(argv) {
@@ -1566,8 +2057,16 @@ async function run(argv) {
     return;
   }
 
+  if (args.mode === 'flow') {
+    await runFlow(process.cwd(), {
+      json: args.json,
+    });
+    return;
+  }
+
   if (args.mode === 'plan') {
     runPlan(process.cwd(), {
+      includeCompleted: args.includeCompleted,
       json: args.json,
       onlyReady: args.onlyReady,
       specSlug: args.specSlug,
@@ -1576,9 +2075,31 @@ async function run(argv) {
     return;
   }
 
+  if (args.mode === 'prepare') {
+    await runPrepare(process.cwd(), {
+      dryRun: args.dryRun,
+      identityFile: args.aiIdentityFile || undefined,
+      provider: args.prepareProvider || undefined,
+      sshHostAlias: args.aiSshHostAlias || undefined,
+    });
+    return;
+  }
+
   if (args.mode === 'ai') {
     if (!args.aiCommand) {
-      throw new Error(formatError('missing ai subcommand. Use: npx create-quiver ai onboard | plan | execute-slice | doctor | pr'));
+      throw new Error(formatError('missing ai subcommand. Use: npx create-quiver ai onboard | prepare-context | plan | review-plan | approve | approvals | agent | prompt-slice | execute-slice | execute-plan | doctor | pr'));
+    }
+
+    if (args.aiCommand === 'agent') {
+      runAiAgent(process.cwd(), {
+        command: args.aiAgentCommand,
+        context: args.aiContext || undefined,
+        label: args.aiLabel || undefined,
+        model: args.aiModel || undefined,
+        provider: args.aiProviderExplicit ? args.aiProvider : undefined,
+        role: args.aiAgentRole || undefined,
+      });
+      return;
     }
 
     if (args.aiCommand === 'onboard') {
@@ -1587,12 +2108,20 @@ async function run(argv) {
         dryRun: args.dryRun,
         input: args.aiInput || undefined,
         provider: args.aiProvider,
+        providerExplicit: args.aiProviderExplicit,
         role: args.aiRole,
         timeout: args.aiTimeout,
       });
       return;
     }
 
+    if (args.aiCommand === 'prepare-context') {
+      await runAiPrepareContext(process.cwd(), {
+        dryRun: args.dryRun,
+      });
+      return;
+    }
+
     if (args.aiCommand === 'plan') {
       await runAiPlan(process.cwd(), {
         context: args.aiContext || undefined,
@@ -1600,6 +2129,7 @@ async function run(argv) {
         input: args.aiInput || undefined,
         phase: args.aiPhase,
         provider: args.aiProvider,
+        providerExplicit: args.aiProviderExplicit,
         role: args.aiRole,
         specSlug: args.specSlug || undefined,
         timeout: args.aiTimeout,
@@ -1607,11 +2137,41 @@ async function run(argv) {
       return;
     }
 
+    if (args.aiCommand === 'review-plan') {
+      await runAiReviewPlan(process.cwd(), {
+        context: args.aiContext || undefined,
+        dryRun: args.dryRun,
+        input: args.aiInput || undefined,
+        provider: args.aiProvider,
+        providerExplicit: args.aiProviderExplicit,
+        timeout: args.aiTimeout,
+      });
+      return;
+    }
+
+    if (args.aiCommand === 'approve') {
+      await runAiApprove(process.cwd(), {
+        dryRun: args.dryRun,
+        input: args.aiInput || undefined,
+        phase: args.aiPhase,
+        version: args.aiVersion || undefined,
+      });
+      return;
+    }
+
+    if (args.aiCommand === 'approvals' || args.aiCommand === 'approval-status') {
+      await runAiApprovalStatus(process.cwd());
+      return;
+    }
+
     if (args.aiCommand === 'execute-slice') {
       await runAiExecuteSlice(process.cwd(), {
+        allowDirty: args.aiAllowDirty,
+        commit: args.aiCommit,
         context: args.aiContext || undefined,
         dryRun: args.dryRun,
         provider: args.aiProvider,
+        providerExplicit: args.aiProviderExplicit,
         role: args.aiRole,
         slice: args.aiSlice || undefined,
         timeout: args.aiTimeout,
@@ -1619,6 +2179,31 @@ async function run(argv) {
       return;
     }
 
+    if (args.aiCommand === 'prompt-slice' || args.aiCommand === 'executor-prompt') {
+      runAiPromptSlice(process.cwd(), {
+        slice: args.aiSlice || undefined,
+      });
+      return;
+    }
+
+    if (args.aiCommand === 'execute-plan') {
+      await runAiExecutePlan(process.cwd(), {
+        allowDirty: args.aiAllowDirty,
+        commit: args.aiCommit,
+        context: args.aiContext || undefined,
+        dryRun: args.dryRun,
+        execute: args.aiExecute,
+        json: args.json,
+        mode: args.aiExecutionMode,
+        provider: args.aiProvider,
+        providerExplicit: args.aiProviderExplicit,
+        role: args.aiRole,
+        specSlug: args.specSlug || undefined,
+        timeout: args.aiTimeout,
+      });
+      return;
+    }
+
     if (args.aiCommand === 'doctor') {
       await runAiDoctor(process.cwd(), {
         dryRun: args.dryRun,
@@ -1631,23 +2216,29 @@ async function run(argv) {
 
     if (args.aiCommand === 'pr') {
       await runAiPr(process.cwd(), {
+        baseBranch: args.aiBaseBranch,
+        create: args.aiCreate,
         dryRun: args.dryRun,
+        input: args.aiInput || undefined,
         remote: args.aiRemote || undefined,
         sshHostAlias: args.aiSshHostAlias || undefined,
         identityFile: args.aiIdentityFile || undefined,
+        title: args.aiTitle || undefined,
       });
       return;
     }
 
-    throw new Error(formatError(`unsupported ai subcommand: ${args.aiCommand}. Supported tasks: onboard, plan, execute-slice, doctor, pr`));
+    throw new Error(formatError(`unsupported ai subcommand: ${args.aiCommand}. Supported tasks: onboard, plan, review-plan, approve, approvals, agent, prompt-slice, execute-slice, execute-plan, doctor, pr`));
   }
 
   if (args.mode === 'graph') {
     runGraph(process.cwd(), {
       format: args.format,
+      includeCompleted: args.includeCompleted,
       json: args.json,
       level: args.level,
       showConflicts: args.showConflicts,
+      specSlug: args.specSlug,
       unicode: args.unicode,
     });
     return;
@@ -1657,19 +2248,45 @@ async function run(argv) {
     await runNext(process.cwd(), {
       allReady: args.allReady,
       autoStart: args.autoStart,
+      includeCompleted: args.includeCompleted,
       json: args.json,
       specSlug: args.specSlug,
     });
     return;
   }
 
+  if (args.mode === 'evidence') {
+    const result = runEvidence(process.cwd(), {
+      command: args.evidenceArgs,
+      maxOutput: args.evidenceMaxOutput || undefined,
+      output: args.evidenceOutput || undefined,
+      subcommand: args.evidenceCommand,
+    });
+    process.exitCode = result.exitCode;
+    return;
+  }
+
+  if (args.mode === 'demo') {
+    const demoTarget = resolveTargetRoot(process.cwd(), args.targetDirExplicit ? args.targetDir : 'quiver-spec-viewer');
+    runDemo({
+      command: args.demoCommand,
+      demo: args.demoName,
+      dryRun: args.dryRun,
+      targetRoot: demoTarget,
+    });
+    return;
+  }
+
   if (args.mode === 'migrate') {
     runMigrate(args.targetDir, { skipInstall: args.skipInstall });
     return;
   }
 
   if (args.mode === 'doctor') {
-    runDoctor(args.targetDir);
+    runDoctor(args.targetDir, {
+      dryRun: args.dryRun,
+      fix: args.doctorFix,
+    });
     return;
   }
 
@@ -1680,7 +2297,10 @@ async function run(argv) {
 
   if (args.mode === 'check-slice') {
     checkSliceReadiness(args.targetDir, {
+      baseBranch: args.baseBranchExplicit ? args.aiBaseBranch : '',
       gate: args.gate,
+      local: args.checkSliceLocal,
+      remote: args.aiRemote,
       strictOverlap: args.strictOverlap,
     });
     return;
@@ -1731,6 +2351,47 @@ async function run(argv) {
     return;
   }
 
+  if (args.mode === 'spec') {
+    if (args.specCommand === 'create') {
+      runCreateSpec(process.cwd(), {
+        dryRun: args.dryRun,
+        input: args.aiInput || undefined,
+        specSlug: args.specSlug || undefined,
+      });
+      return;
+    }
+
+    if (!args.targetDir || args.targetDir === '.') {
+      throw new Error(formatError('missing spec directory. Use: npx create-quiver spec <start|status|close> <spec-dir>'));
+    }
+
+    if (args.specCommand === 'start') {
+      const report = startSpecWorktree(process.cwd(), args.targetDir);
+      process.stdout.write(formatSpecStartResult(report));
+      return;
+    }
+
+    if (args.specCommand === 'status') {
+      const report = buildSpecStatus(process.cwd(), args.targetDir);
+      process.stdout.write(formatSpecStatus(report));
+      return;
+    }
+
+    if (args.specCommand === 'close') {
+      const report = closeSpecWorktree(process.cwd(), args.targetDir, {
+        baseBranch: args.aiBaseBranch,
+        discard: args.discard,
+        dryRun: args.dryRun,
+        force: args.force,
+        remote: args.aiRemote,
+      });
+      process.stdout.write(formatSpecCloseResult(report));
+      return;
+    }
+
+    throw new Error(formatError(`unsupported spec subcommand: ${args.specCommand}. Supported tasks: create, start, status, close`));
+  }
+
   const packageRoot = path.resolve(__dirname, '../..');
   const targetDir = resolveTargetRoot(process.cwd(), args.targetDir);
   const projectName = args.projectName || path.basename(targetDir) || 'Quiver Project';
@@ -1785,6 +2446,8 @@ async function run(argv) {
 module.exports = {
   runAnalyze,
   runDoctor,
+  runFlow,
   runMigrate,
+  runPrepare,
   run,
 };