atomism 0.1.0

package/dist/workflow-5UVLBS7J.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/commands/workflow.ts"],"sourcesContent":["/**\n * Workflow command implementation for the atomic CLI.\n *\n * This module implements workflow execution commands including\n * `atomic workflow run` with dependency resolution and progress display.\n *\n * @module commands/workflow\n */\n\nimport { join } from 'node:path';\nimport { readFile, readdir } from 'node:fs/promises';\nimport { z } from 'zod';\nimport { ATOMIC_DIR, fileExists } from '../storage/index.js';\nimport { executeAtom } from '../atom/execute.js';\nimport {\n  AtomWithArtifacts,\n  createArtifactCache,\n  resolveDependencies,\n  formatDependencyChain,\n  type ResolvedAtom,\n  type ResolutionResult,\n} from '../workflow/index.js';\nimport {\n  saveRunState,\n  loadRunState,\n  updateAtomState,\n  getResumableAtoms,\n  getLastFailedRun,\n  createRunState,\n  type WorkflowRunState,\n  type BeadOptions,\n} from '../workflow/run-state.js';\nimport {\n  isBeadsAvailable,\n  isBeadsInitialized,\n  createWorkflowBeads,\n  updateAtomBead,\n  updateWorkflowBead,\n} from '../workflow/beads.js';\nimport { WorkflowDefinition } from '../schemas/workflow.js';\nimport { fmt } from '../cli/format.js';\nimport { toErrorMessage } from '../utils/errors.js';\n\ntype AtomWithArtifactsType = z.infer<typeof AtomWithArtifacts>;\ntype WorkflowDefinitionType = z.infer<typeof WorkflowDefinition>;\n\n/**\n * Result accumulator for the shared execution loop.\n * Both run and resume commands populate this during atom execution.\n */\ninterface ExecutionAccumulator {\n  success: boolean;\n  executed: string[];\n  errors: Array<{ atom: string; error: string }>;\n  /** Optional artifact tracking (used by run, not by resume) */\n  artifacts?: Record<string, string[]>;\n}\n\n/**\n * Execute a sequence of workflow atoms, updating run state and beads as each completes.\n *\n * This is the shared execution loop used by both `workflowRunCommand` and\n * `workflowResumeCommand`. Each caller sets up its own initialization\n * (fresh state vs loaded state) and calls this function for the actual execution.\n *\n * @param atomIds - Ordered list of atom IDs to execute\n * @param atoms - Full atom definitions (used to look up atom names and artifact declarations)\n * @param runState - Mutable run state, updated in place as atoms execute\n * @param accumulator - Mutable result accumulator, updated in place\n * @param options - Display options\n * @param resolvedAtoms - Optional resolved atoms from dependency resolution (provides per-atom artifact inputs)\n */\nasync function executeWorkflowAtoms(\n  atomIds: string[],\n  atoms: AtomWithArtifactsType[],\n  runState: WorkflowRunState,\n  accumulator: ExecutionAccumulator,\n  options: { json?: boolean },\n  resolvedAtoms?: ResolvedAtom[],\n): Promise<void> {\n  for (const id of atomIds) {\n    const atom = atoms.find((a) => (a.alias ?? a.atom) === id);\n    const atomState = runState.atoms.find((a) => a.id === id);\n\n    if (!options.json) {\n      process.stdout.write(`  ${fmt.gray('○')} ${id}...`);\n    }\n\n    // Update bead to in_progress\n    if (runState.beadsEnabled && atomState?.beadId) {\n      await updateAtomBead(atomState.beadId, 'in_progress');\n    }\n\n    // Update run state to running\n    updateAtomState(runState, id, {\n      status: 'running',\n      startedAt: new Date().toISOString(),\n    });\n    await saveRunState(runState);\n\n    try {\n      // Build per-atom input from resolved artifact dependencies.\n      // Each resolved atom carries an `inputs` map (field name -> CachedArtifact);\n      // we extract the `content` from each artifact to form the input object.\n      const resolvedForAtom = resolvedAtoms?.find((r) => r.id === id);\n      const atomInput: Record<string, unknown> = {};\n      if (resolvedForAtom) {\n        for (const [fieldName, cachedArtifact] of resolvedForAtom.inputs) {\n          atomInput[fieldName] = cachedArtifact.content;\n        }\n      }\n\n      const atomResult = await executeAtom(\n        atom?.atom ?? id,\n        atomInput,\n        process.cwd()\n      );\n\n      if (!atomResult.success) {\n        throw new Error(atomResult.error ?? 'Atom execution failed');\n      }\n\n      accumulator.executed.push(id);\n\n      // Record actual artifacts from execution\n      const producedArtifacts = atom?.produces?.map((p) => p.artifact);\n      if (accumulator.artifacts && producedArtifacts && producedArtifacts.length > 0) {\n        accumulator.artifacts[id] = producedArtifacts;\n      }\n\n      // Update run state to completed\n      updateAtomState(runState, id, {\n        status: 'completed',\n        completedAt: new Date().toISOString(),\n        artifacts: producedArtifacts,\n      });\n      await saveRunState(runState);\n\n      // Update bead to completed\n      if (runState.beadsEnabled && atomState?.beadId) {\n        await updateAtomBead(atomState.beadId, 'completed');\n      }\n\n      if (!options.json) {\n        // Clear the line and show success\n        process.stdout.write(`\\r  ${fmt.green('✓')} ${id}    \\n`);\n      }\n    } catch (err) {\n      const errMsg = toErrorMessage(err);\n      accumulator.success = false;\n      accumulator.errors.push({\n        atom: id,\n        error: errMsg,\n      });\n\n      // Update run state to failed\n      updateAtomState(runState, id, {\n        status: 'failed',\n        error: errMsg,\n      });\n      runState.status = 'failed';\n      runState.failedAtom = id;\n      runState.error = errMsg;\n      await saveRunState(runState);\n\n      // Update bead to failed\n      if (runState.beadsEnabled && atomState?.beadId) {\n        await updateAtomBead(atomState.beadId, 'failed', errMsg);\n      }\n\n      if (!options.json) {\n        // Clear the line and show failure\n        process.stdout.write(`\\r  ${fmt.red('✗')} ${id}: ${errMsg}    \\n`);\n      }\n\n      // Stop execution on failure\n      break;\n    }\n  }\n}\n\n/**\n * Options for the workflow run command.\n */\nexport interface WorkflowRunOptions {\n  dryRun?: boolean;\n  json?: boolean;\n  forceRebuild?: string;\n  forceRebuildAll?: boolean;\n  /** Beads tracking (default: true, use --no-beads to disable) */\n  beads?: boolean;\n}\n\n/**\n * Workflow file stored in .atomic/workflows/\n */\ninterface StoredWorkflow {\n  definition: WorkflowDefinitionType;\n  atoms: AtomWithArtifactsType[];\n}\n\n/**\n * Result of workflow execution.\n */\nexport interface WorkflowRunResult {\n  success: boolean;\n  workflow: string;\n  executionOrder: string[];\n  skipped: string[];\n  executed: string[];\n  artifacts: Record<string, string[]>;\n  errors: Array<{ atom: string; error: string }>;\n  duration: number;\n}\n\nconst WORKFLOWS_DIR = 'workflows';\nconst WORKFLOW_EXT = '.workflow.json';\n\n/**\n * Load a workflow from the .atomic/workflows/ directory.\n */\nasync function loadWorkflow(name: string): Promise<StoredWorkflow> {\n  const projectRoot = process.cwd();\n  const workflowPath = join(\n    projectRoot,\n    ATOMIC_DIR,\n    WORKFLOWS_DIR,\n    `${name}${WORKFLOW_EXT}`\n  );\n\n  if (!(await fileExists(workflowPath))) {\n    throw new Error(\n      `Workflow '${name}' not found.\\n` +\n        `Expected file: ${workflowPath}`\n    );\n  }\n\n  const content = await readFile(workflowPath, 'utf-8');\n\n  // Parse JSON with clear error message\n  let data: unknown;\n  try {\n    data = JSON.parse(content);\n  } catch (err) {\n    throw new Error(\n      `Workflow '${name}' contains invalid JSON: ${toErrorMessage(err)}`\n    );\n  }\n\n  // Validate the workflow definition\n  const parsed = data as { definition?: unknown; atoms?: unknown; capabilities?: unknown };\n  const definition = WorkflowDefinition.parse(parsed.definition);\n\n  // Support both 'atoms' (new) and 'capabilities' (deprecated) for migration\n  const atomsData = parsed.atoms ?? parsed.capabilities;\n\n  // Validate atoms array exists\n  if (!Array.isArray(atomsData)) {\n    throw new Error(`Workflow '${name}' has invalid atoms structure`);\n  }\n\n  // Validate each atom using the schema\n  const atoms = atomsData.map((atom: unknown, index: number) => {\n    try {\n      return AtomWithArtifacts.parse(atom);\n    } catch (err) {\n      throw new Error(\n        `Workflow '${name}' has invalid atom at index ${index}: ${toErrorMessage(err)}`\n      );\n    }\n  });\n\n  return { definition, atoms };\n}\n\n/**\n * Convert workflow atoms to resolver format.\n */\nfunction convertToResolverAtoms(\n  workflow: WorkflowDefinitionType,\n  atoms: AtomWithArtifactsType[]\n): AtomWithArtifactsType[] {\n  // If atoms are provided, use them directly\n  if (atoms.length > 0) {\n    return atoms;\n  }\n\n  // Otherwise, convert from WorkflowDefinition format\n  return workflow.atoms.map((a) => ({\n    atom: a.atom,\n    dependsOn: a.dependsOn,\n    alias: a.alias,\n    description: a.description,\n    requires: [],\n    produces: [],\n  }));\n}\n\n/**\n * Format workflow run result for display.\n */\nfunction formatWorkflowResult(result: WorkflowRunResult): string {\n  const lines: string[] = [];\n\n  if (result.success) {\n    lines.push(\n      fmt.green('✓') + fmt.bold(` Workflow '${result.workflow}' completed`)\n    );\n  } else {\n    lines.push(\n      fmt.red('✗') + fmt.bold(` Workflow '${result.workflow}' failed`)\n    );\n  }\n\n  lines.push('');\n  lines.push(fmt.gray(`Duration: ${result.duration}ms`));\n  lines.push('');\n\n  // Execution summary\n  lines.push(fmt.bold('Execution Summary:'));\n  lines.push(`  Executed: ${result.executed.length} atoms`);\n  lines.push(`  Skipped:  ${result.skipped.length} atoms (cached)`);\n\n  if (result.executed.length > 0) {\n    lines.push('');\n    lines.push(fmt.bold('Executed:'));\n    for (const atomId of result.executed) {\n      lines.push(`  ${fmt.green('✓')} ${atomId}`);\n    }\n  }\n\n  if (result.skipped.length > 0) {\n    lines.push('');\n    lines.push(fmt.bold('Skipped (cached):'));\n    for (const atomId of result.skipped) {\n      lines.push(`  ${fmt.gray('○')} ${atomId}`);\n    }\n  }\n\n  if (result.errors.length > 0) {\n    lines.push('');\n    lines.push(fmt.bold(fmt.red('Errors:')));\n    for (const { atom, error } of result.errors) {\n      lines.push(`  ${fmt.red('✗')} ${atom}: ${error}`);\n    }\n  }\n\n  // Artifacts produced\n  const artifactCount = Object.values(result.artifacts).flat().length;\n  if (artifactCount > 0) {\n    lines.push('');\n    lines.push(fmt.bold(`Artifacts Produced (${artifactCount}):`));\n    for (const [atomId, artifacts] of Object.entries(result.artifacts)) {\n      for (const artifact of artifacts) {\n        lines.push(`  ${fmt.cyan('→')} ${atomId}/${artifact}`);\n      }\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format dry-run output for display.\n */\nfunction formatDryRun(\n  workflow: string,\n  resolution: ResolutionResult,\n  atoms: AtomWithArtifactsType[]\n): string {\n  const lines: string[] = [];\n\n  lines.push(fmt.bold(`Dry Run: Workflow '${workflow}'`));\n  lines.push('');\n\n  // Show dependency chain\n  lines.push(fmt.bold('Resolving dependencies:'));\n  lines.push(`  ${formatDependencyChain(resolution.toExecute)}`);\n  lines.push('');\n\n  // Execution plan\n  lines.push(fmt.bold('Execution Plan:'));\n  let step = 1;\n  for (const id of resolution.toExecute) {\n    const resolved = resolution.resolved.find((r) => r.id === id);\n    const atom = atoms.find(\n      (a) => (a.alias ?? a.atom) === id\n    );\n    const reason = resolved?.reason ?? 'Will execute';\n    lines.push(`  ${step}. ${fmt.cyan(id)}`);\n    if (atom?.description) {\n      lines.push(`     ${fmt.gray(atom.description)}`);\n    }\n    lines.push(`     ${fmt.gray(`Reason: ${reason}`)}`);\n    step++;\n  }\n\n  // Skipped atoms\n  if (resolution.skipped.length > 0) {\n    lines.push('');\n    lines.push(fmt.bold('Will Skip (cached):'));\n    for (const id of resolution.skipped) {\n      const resolved = resolution.resolved.find((r) => r.id === id);\n      lines.push(`  ${fmt.gray('○')} ${id} - ${resolved?.reason ?? 'Cached'}`);\n    }\n  }\n\n  // Artifacts that will be produced\n  lines.push('');\n  lines.push(fmt.bold('Expected Artifacts:'));\n  for (const atom of atoms) {\n    const id = atom.alias ?? atom.atom;\n    if (atom.produces.length > 0 && resolution.toExecute.includes(id)) {\n      for (const prod of atom.produces) {\n        lines.push(`  ${fmt.cyan('→')} ${id}/${prod.artifact}`);\n      }\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Execute a workflow with the given name.\n *\n * @param name - The workflow name to execute\n * @param options - Execution options\n */\nexport async function workflowRunCommand(\n  name: string,\n  options: WorkflowRunOptions\n): Promise<void> {\n  const startTime = Date.now();\n\n  try {\n    // Load workflow\n    const { definition, atoms: storedAtoms } =\n      await loadWorkflow(name);\n    const atoms = convertToResolverAtoms(\n      definition,\n      storedAtoms\n    );\n\n    // Create cache (in-memory for now)\n    const cache = createArtifactCache();\n\n    // Parse forceRebuild option, filtering empty strings from trailing commas\n    const forceRebuild = options.forceRebuild\n      ? options.forceRebuild\n          .split(',')\n          .map((s) => s.trim())\n          .filter((s) => s.length > 0)\n      : [];\n\n    // Resolve dependencies\n    const resolution = resolveDependencies(atoms, {\n      cache,\n      forceRebuild,\n      forceRebuildAll: options.forceRebuildAll,\n    });\n\n    // Dry run mode - just show the plan\n    if (options.dryRun) {\n      if (options.json) {\n        const dryRunResult = {\n          workflow: name,\n          dryRun: true,\n          executionOrder: resolution.toExecute,\n          skipped: resolution.skipped,\n          resolved: resolution.resolved.map((r) => ({\n            id: r.id,\n            canSkip: r.canSkip,\n            reason: r.reason,\n            inputs: Array.from(r.inputs.keys()),\n          })),\n        };\n        console.log(JSON.stringify(dryRunResult, null, 2));\n      } else {\n        console.log(formatDryRun(name, resolution, atoms));\n      }\n      return;\n    }\n\n    // Setup beads tracking (default: enabled, unless --no-beads or dry-run)\n    const beadsEnabled = options.beads !== false && !options.dryRun;\n    let beadOptions: BeadOptions | undefined;\n\n    if (beadsEnabled) {\n      // Check if beads is available and initialized\n      if (!(await isBeadsAvailable())) {\n        if (!options.json) {\n          console.log(fmt.yellow('⚠'), fmt.gray('Beads CLI not found, skipping tracking'));\n        }\n      } else if (!(await isBeadsInitialized())) {\n        if (!options.json) {\n          console.log(fmt.yellow('⚠'), fmt.gray('Beads not initialized, skipping tracking'));\n        }\n      } else {\n        // Create workflow beads\n        const beadsResult = await createWorkflowBeads({\n          workflow: name,\n          description: definition.description,\n          atoms: resolution.toExecute,\n        });\n\n        if (beadsResult.success) {\n          beadOptions = {\n            enabled: true,\n            parentId: beadsResult.parentId,\n            atomBeadIds: beadsResult.childIds,\n          };\n          if (!options.json) {\n            console.log(fmt.cyan('⊙'), fmt.gray(`Beads tracking: ${beadsResult.parentId}`));\n          }\n        } else if (!options.json) {\n          console.log(fmt.yellow('⚠'), fmt.gray(`Beads error: ${beadsResult.error}`));\n        }\n      }\n    }\n\n    // Create run state for tracking\n    const runState = createRunState(\n      name,\n      resolution.toExecute,\n      resolution.skipped,\n      beadOptions\n    );\n    await saveRunState(runState);\n\n    // Execute workflow\n    const result: WorkflowRunResult = {\n      success: true,\n      workflow: name,\n      executionOrder: resolution.toExecute,\n      skipped: resolution.skipped,\n      executed: [],\n      artifacts: {},\n      errors: [],\n      duration: 0,\n    };\n\n    // Show progress header\n    if (!options.json) {\n      console.log(fmt.bold(`Executing Workflow: ${name}`));\n      console.log(\n        `${fmt.gray('Resolving dependencies:')} ${formatDependencyChain(resolution.toExecute)}`\n      );\n      console.log('');\n    }\n\n    // Execute each atom in order, passing resolved artifact inputs\n    await executeWorkflowAtoms(\n      resolution.toExecute,\n      atoms,\n      runState,\n      result,\n      { json: options.json },\n      resolution.resolved,\n    );\n\n    // Update final run state\n    if (result.success) {\n      runState.status = 'completed';\n      runState.completedAt = new Date().toISOString();\n    }\n    await saveRunState(runState);\n\n    // Update workflow bead\n    if (runState.beadParentId) {\n      await updateWorkflowBead(runState.beadParentId, result.success, runState.failedAtom);\n    }\n\n    result.duration = Date.now() - startTime;\n\n    // Output result\n    if (options.json) {\n      console.log(JSON.stringify(result, null, 2));\n    } else {\n      console.log('');\n      console.log(formatWorkflowResult(result));\n    }\n\n    if (!result.success) {\n      process.exit(1);\n    }\n  } catch (err) {\n    const duration = Date.now() - startTime;\n\n    if (options.json) {\n      console.log(\n        JSON.stringify(\n          {\n            success: false,\n            workflow: name,\n            error: toErrorMessage(err),\n            duration,\n          },\n          null,\n          2\n        )\n      );\n    } else {\n      console.error(\n        fmt.red('Error:'),\n        toErrorMessage(err)\n      );\n    }\n    process.exit(1);\n  }\n}\n\n/**\n * List available workflows.\n */\nexport async function workflowListCommand(options: {\n  json?: boolean;\n}): Promise<void> {\n  const projectRoot = process.cwd();\n  const workflowsDir = join(projectRoot, ATOMIC_DIR, WORKFLOWS_DIR);\n\n  try {\n    if (!(await fileExists(workflowsDir))) {\n      if (options.json) {\n        console.log(JSON.stringify({ workflows: [] }, null, 2));\n      } else {\n        console.log(fmt.gray('No workflows directory found.'));\n        console.log(\n          fmt.gray(`Create workflows in ${ATOMIC_DIR}/${WORKFLOWS_DIR}/`)\n        );\n      }\n      return;\n    }\n\n    // Read workflow files\n    const files = await readdir(workflowsDir);\n    const workflowFiles = files.filter((f) => f.endsWith(WORKFLOW_EXT));\n\n    if (workflowFiles.length === 0) {\n      if (options.json) {\n        console.log(JSON.stringify({ workflows: [] }, null, 2));\n      } else {\n        console.log(fmt.gray('No workflows found.'));\n      }\n      return;\n    }\n\n    // Load workflow metadata\n    const workflows: Array<{\n      name: string;\n      description: string;\n      atoms: number;\n    }> = [];\n\n    for (const file of workflowFiles) {\n      const name = file.replace(WORKFLOW_EXT, '');\n      try {\n        const { definition } = await loadWorkflow(name);\n        workflows.push({\n          name,\n          description: definition.description,\n          atoms: definition.atoms.length,\n        });\n      } catch (err) {\n        // Log warning for invalid workflows (unless JSON mode)\n        if (!options.json) {\n          console.error(\n            fmt.yellow('Warning:'),\n            `Could not load workflow '${name}': ${toErrorMessage(err)}`\n          );\n        }\n      }\n    }\n\n    if (options.json) {\n      console.log(JSON.stringify({ workflows }, null, 2));\n    } else {\n      console.log(fmt.bold('Available Workflows:'));\n      console.log('');\n      for (const wf of workflows) {\n        console.log(`  ${fmt.cyan(wf.name)}`);\n        console.log(`    ${wf.description}`);\n        console.log(`    ${fmt.gray(`${wf.atoms} atoms`)}`);\n        console.log('');\n      }\n    }\n  } catch (err) {\n    if (options.json) {\n      console.log(\n        JSON.stringify(\n          {\n            error: toErrorMessage(err),\n          },\n          null,\n          2\n        )\n      );\n    } else {\n      console.error(\n        fmt.red('Error:'),\n        toErrorMessage(err)\n      );\n    }\n    process.exit(1);\n  }\n}\n\n/**\n * Options for the workflow resume command.\n */\nexport interface WorkflowResumeOptions {\n  run?: string;\n  from?: string;\n  json?: boolean;\n  /** Beads tracking (default: true, use --no-beads to disable) */\n  beads?: boolean;\n}\n\n/**\n * Resume result for JSON output.\n */\nexport interface WorkflowResumeResult {\n  success: boolean;\n  workflow: string;\n  runId: string;\n  resumedFrom: string;\n  executed: string[];\n  skipped: string[];\n  errors: Array<{ atom: string; error: string }>;\n  duration: number;\n}\n\n/**\n * Resume a failed or partial workflow execution.\n *\n * @param name - The workflow name to resume\n * @param options - Resume options\n */\nexport async function workflowResumeCommand(\n  name: string,\n  options: WorkflowResumeOptions\n): Promise<void> {\n  const startTime = Date.now();\n\n  try {\n    // Load workflow definition\n    const { definition, atoms: storedAtoms } =\n      await loadWorkflow(name);\n    const atoms = convertToResolverAtoms(\n      definition,\n      storedAtoms\n    );\n\n    // Find the run state to resume\n    let runState: WorkflowRunState | null = null;\n\n    if (options.run) {\n      runState = await loadRunState(options.run);\n      if (!runState) {\n        throw new Error(`Run '${options.run}' not found`);\n      }\n      if (runState.workflow !== name) {\n        throw new Error(\n          `Run '${options.run}' is for workflow '${runState.workflow}', not '${name}'`\n        );\n      }\n    } else {\n      // Find the last failed run for this workflow\n      runState = await getLastFailedRun(name);\n      if (!runState) {\n        throw new Error(\n          `No failed runs found for workflow '${name}'. Use --run to specify a run ID.`\n        );\n      }\n    }\n\n    // Determine which atoms to execute\n    const toExecute = getResumableAtoms(runState, options.from);\n\n    if (toExecute.length === 0) {\n      if (options.json) {\n        console.log(\n          JSON.stringify(\n            {\n              success: true,\n              workflow: name,\n              runId: runState.runId,\n              message: 'No atoms need to be executed',\n            },\n            null,\n            2\n          )\n        );\n      } else {\n        console.log(\n          fmt.green('✓'),\n          `Workflow '${name}' has no atoms to resume`\n        );\n      }\n      return;\n    }\n\n    // Determine what was already completed\n    const alreadyCompleted = runState.executionOrder.filter(\n      (id) => !toExecute.includes(id)\n    );\n\n    // Handle beads tracking for resume\n    // If --no-beads, disable beads regardless of original run\n    // If original run had beads, reuse them\n    // If original run didn't have beads and --no-beads not set, create new ones\n    const beadsDisabled = options.beads === false;\n\n    if (!beadsDisabled && !runState.beadsEnabled) {\n      // Original run didn't have beads, try to create new ones\n      if ((await isBeadsAvailable()) && (await isBeadsInitialized())) {\n        const beadsResult = await createWorkflowBeads({\n          workflow: name,\n          description: definition.description,\n          atoms: toExecute,\n        });\n\n        if (beadsResult.success) {\n          runState.beadsEnabled = true;\n          runState.beadParentId = beadsResult.parentId;\n          // Update atom bead IDs\n          for (const id of toExecute) {\n            const beadId = beadsResult.childIds.get(id);\n            if (beadId) {\n              updateAtomState(runState, id, { beadId });\n            }\n          }\n          if (!options.json) {\n            console.log(fmt.cyan('⊙'), fmt.gray(`Beads tracking: ${beadsResult.parentId}`));\n          }\n        }\n      }\n    } else if (!beadsDisabled && runState.beadsEnabled) {\n      // Reuse existing beads\n      if (!options.json && runState.beadParentId) {\n        console.log(fmt.cyan('⊙'), fmt.gray(`Beads tracking: ${runState.beadParentId} (resumed)`));\n      }\n    }\n\n    const result: WorkflowResumeResult = {\n      success: true,\n      workflow: name,\n      runId: runState.runId,\n      resumedFrom: toExecute[0]!,\n      executed: [],\n      skipped: alreadyCompleted,\n      errors: [],\n      duration: 0,\n    };\n\n    // Show progress header\n    if (!options.json) {\n      console.log(fmt.bold(`Resuming Workflow: ${name}`));\n      console.log(`${fmt.gray('Run ID:')} ${runState.runId}`);\n      console.log(\n        `${fmt.gray('Skipping completed:')} ${alreadyCompleted.length > 0 ? alreadyCompleted.join(', ') : 'none'}`\n      );\n      console.log(`${fmt.gray('Resuming from:')} ${toExecute[0]}`);\n      console.log('');\n    }\n\n    // Update run state to running\n    runState.status = 'running';\n    await saveRunState(runState);\n\n    // Execute remaining atoms\n    await executeWorkflowAtoms(\n      toExecute,\n      atoms,\n      runState,\n      result,\n      { json: options.json },\n    );\n\n    // Update final run state\n    if (result.success) {\n      runState.status = 'completed';\n      runState.completedAt = new Date().toISOString();\n    }\n    await saveRunState(runState);\n\n    // Update workflow bead\n    if (runState.beadsEnabled && runState.beadParentId) {\n      await updateWorkflowBead(runState.beadParentId, result.success, runState.failedAtom);\n    }\n\n    result.duration = Date.now() - startTime;\n\n    // Output result\n    if (options.json) {\n      console.log(JSON.stringify(result, null, 2));\n    } else {\n      console.log('');\n      if (result.success) {\n        console.log(\n          fmt.green('✓') + fmt.bold(` Workflow '${name}' resumed successfully`)\n        );\n      } else {\n        console.log(\n          fmt.red('✗') + fmt.bold(` Workflow '${name}' resume failed`)\n        );\n      }\n      console.log('');\n      console.log(fmt.gray(`Duration: ${result.duration}ms`));\n      console.log(\n        fmt.gray(`Skipped: ${result.skipped.length} (already completed)`)\n      );\n      console.log(fmt.gray(`Executed: ${result.executed.length}`));\n\n      if (result.errors.length > 0) {\n        console.log('');\n        console.log(fmt.bold(fmt.red('Errors:')));\n        for (const { atom, error } of result.errors) {\n          console.log(`  ${fmt.red('✗')} ${atom}: ${error}`);\n        }\n      }\n    }\n\n    if (!result.success) {\n      process.exit(1);\n    }\n  } catch (err) {\n    const duration = Date.now() - startTime;\n\n    if (options.json) {\n      console.log(\n        JSON.stringify(\n          {\n            success: false,\n            workflow: name,\n            error: toErrorMessage(err),\n            duration,\n      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package/package.json

@@ -0,0 +1,84 @@
+{
+  "name": "atomism",
+  "version": "0.1.0",
+  "description": "Schema-first agent swarm orchestration framework",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js"
+    }
+  },
+  "bin": {
+    "atomic": "dist/cli.js"
+  },
+  "files": [
+    "dist",
+    "README.md",
+    "LICENSE"
+  ],
+  "scripts": {
+    "build": "tsup",
+    "dev": "tsx src/cli.ts",
+    "docs:dev": "vitepress dev docs",
+    "docs:build": "vitepress build docs",
+    "docs:preview": "vitepress preview docs",
+    "lint": "eslint src/",
+    "lint:fix": "eslint src/ --fix",
+    "test": "vitest",
+    "typecheck": "tsc --noEmit"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/Trust-Will/atomic-explore.git"
+  },
+  "keywords": [
+    "cli",
+    "agent",
+    "swarm",
+    "orchestration",
+    "schema",
+    "zod",
+    "ai",
+    "llm",
+    "workflow",
+    "automation",
+    "claude",
+    "atoms"
+  ],
+  "author": "",
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/Trust-Will/atomic-explore/issues"
+  },
+  "homepage": "https://github.com/Trust-Will/atomic-explore#readme",
+  "engines": {
+    "node": ">=18"
+  },
+  "dependencies": {
+    "@tursodatabase/database": "^0.4.4",
+    "@vscode/tree-sitter-wasm": "^0.3.0",
+    "commander": "^14.0.2",
+    "edit-distance": "^1.0.5",
+    "jiti": "^2.6.1",
+    "oxc-parser": "^0.111.0",
+    "web-tree-sitter": "^0.26.3",
+    "zod": "^4.3.6",
+    "zod-to-json-schema": "^3.25.1"
+  },
+  "devDependencies": {
+    "@eslint/js": "^9.39.2",
+    "@types/node": "^25.1.0",
+    "@typescript-eslint/eslint-plugin": "^8.54.0",
+    "@typescript-eslint/parser": "^8.54.0",
+    "eslint": "^9.39.2",
+    "tsup": "^8.5.1",
+    "tsx": "^4.21.0",
+    "typescript": "^5.9.3",
+    "typescript-eslint": "^8.54.0",
+    "vitepress": "^1.6.4",
+    "vitest": "^4.0.18"
+  }
+}