atomism 0.1.0 → 0.1.2

package/README.md

@@ -199,11 +199,11 @@ executionError('Runtime failure')     // Execution error
 
 ## Documentation
 
-Full documentation: https://trust-will.github.io/atomic-explore/
+Full documentation: https://github.com/roach88/atomism
 
 ## Requirements
 
-- Node.js 18+
+- Node.js 20+
 
 ## License
 

package/dist/cli.js

@@ -5,7 +5,7 @@ import { Command } from "commander";
 var program = new Command();
 program.name("atomic").description("Schema-first agent swarm orchestration framework").version("0.1.0");
 program.command("init").description("Initialize .atomic/ directory with storage and registry").option("--json", "Output structured JSON response").action(async (options) => {
-  const { initCommand } = await import("./init-2FINDMYK.js");
+  const { initCommand } = await import("./init-EH6ZWP5R.js");
   return initCommand(options);
 });
 program.command("register <path>").description("Register an atom file").option("--json", "Output structured JSON response").action(async (atomPath, options) => {
@@ -42,7 +42,7 @@ create.command("atom <name>").description("Create a new atom with scaffolded fil
   return createAtomCommand(name, options);
 });
 program.command("extract").description("Extract atom from existing skill, BMAD workflow, MCP tool, or code").option("--skill <path>", "Extract from Claude Code skill").option("--bmad <path>", "Extract from BMAD workflow").option("--mcp <path>", "Extract from MCP tool definition").option("--code <path>", "Extract from existing code file").option("--output <dir>", "Output directory for generated atom").option("-y, --yes", "Auto-create without confirmation").option("--json", "Output structured JSON response").action(async (options) => {
-  const { extractCommand } = await import("./extract-RPKCTINT.js");
+  const { extractCommand } = await import("./extract-6WTZGLKX.js");
   return extractCommand(options);
 });
 program.command("suggest").description("Scan codebase for functions that could become atoms").option("--path <dir>", "Directory to scan (default: cwd)").option("--limit <n>", "Max candidates to show (default: 20)").option("--scan-limit <n>", "Max files to scan (default: 1000)").option("--json", "Output structured JSON response").action(async (options) => {

package/dist/{extract-RPKCTINT.js → extract-6WTZGLKX.js}

@@ -468,7 +468,7 @@ async function extractCommand(options) {
     const testPath = join(outputDir, `${extracted.name}.test.ts`);
     const resolvedOutputDir = resolve(outputDir);
     const rel = relative(resolvedOutputDir, resolve(atomPath));
-    if (rel.startsWith("..") || isAbsolute(rel)) {
+    if (isAbsolute(rel) || rel.startsWith("..")) {
       throw new Error("Generated path escapes output directory");
     }
     if (await fileExists(atomPath)) {
@@ -511,4 +511,4 @@ export {
   escapeSourcePath,
   extractCommand
 };
-//# sourceMappingURL=extract-RPKCTINT.js.map
+//# sourceMappingURL=extract-6WTZGLKX.js.map

package/dist/{extract-RPKCTINT.js.map → extract-6WTZGLKX.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/commands/extract.ts"],"sourcesContent":["/**\n * Extract command - Create atoms from existing sources.\n *\n * Story 1.10: AOP-1216\n *\n * Acceptance Criteria:\n * - Extract from Claude Code skills, BMAD workflows, MCP tools, or code\n * - Analyze source for input parameters, output format, description\n * - Display proposed atom definition for user approval\n * - Create atom file with extracted structure\n */\n\nimport { readFile, stat, mkdir, writeFile } from 'node:fs/promises';\nimport { join, basename, dirname, resolve, relative, isAbsolute } from 'node:path';\nimport { fmt } from '../cli/format.js';\nimport { initStorage, ATOMIC_DIR, fileExists } from '../storage/index.js';\nimport { toErrorMessage } from '../utils/errors.js';\nimport { resolveAtomPath } from '../utils/paths.js';\n\n/**\n * Options for the extract command.\n */\nexport interface ExtractOptions {\n  skill?: string;\n  bmad?: string;\n  mcp?: string;\n  code?: string;\n  output?: string;\n  yes?: boolean;\n  json?: boolean;\n}\n\n/**\n * A single extracted field with human-readable type and Zod code-gen token.\n */\nexport interface ExtractedField {\n  name: string;\n  type: string;       // human label: 'string', 'number', etc.\n  zodType: string;    // code-gen token: 'z.string()', 'z.number()', etc.\n  description: string;\n}\n\n/**\n * Extracted atom definition.\n */\nexport interface ExtractedAtom {\n  name: string;\n  description: string;\n  inputFields: ExtractedField[];\n  outputFields: ExtractedField[];\n  sourceType: 'skill' | 'bmad' | 'mcp' | 'code';\n  sourcePath: string;\n}\n\n/**\n * Result of extraction.\n */\nexport interface ExtractResult {\n  success: boolean;\n  extracted?: ExtractedAtom;\n  atomPath?: string;\n  testPath?: string;\n  error?: string;\n}\n\n/**\n * Parse YAML frontmatter from markdown content.\n *\n * Note: This is a simple parser that handles basic key: value pairs.\n * It does not support quoted values with colons, multi-line strings,\n * or nested structures. For complex YAML, consider using a proper parser.\n */\nfunction parseFrontmatter(content: string): Record<string, string> {\n  const match = content.match(/^---\\n([\\s\\S]*?)\\n---/);\n  if (!match || !match[1]) {\n    return {};\n  }\n\n  const frontmatter: Record<string, string> = {};\n  const lines = match[1].split('\\n');\n\n  for (const line of lines) {\n    const colonIndex = line.indexOf(':');\n    if (colonIndex > 0) {\n      const key = line.substring(0, colonIndex).trim();\n      const value = line.substring(colonIndex + 1).trim();\n      frontmatter[key] = value;\n    }\n  }\n\n  return frontmatter;\n}\n\n/**\n * Convert a name to snake_case.\n */\nfunction toSnakeCase(name: string): string {\n  return name\n    .replace(/[^a-zA-Z0-9]+/g, '_')\n    .replace(/([a-z])([A-Z])/g, '$1_$2')\n    .toLowerCase()\n    .replace(/^_+|_+$/g, '')\n    .replace(/_+/g, '_');\n}\n\n/** Valid JS identifier pattern for field names in generated code. */\nconst VALID_JS_IDENTIFIER = /^[a-zA-Z_$][a-zA-Z0-9_$]*$/;\n\n/**\n * Validate that a zodType string is a safe Zod expression.\n * zodType is injected as raw code — structural validation prevents code injection.\n * Matches only the patterns produced by tsTypeToZodType/jsonSchemaTypeToZodType:\n *   z.method()                          — z.string(), z.number(), etc.\n *   z.method(z.method())                — z.array(z.string())\n *   z.method(z.method(), z.method())    — z.record(z.string(), z.number())\n *   z.enum([\"a\", \"b\"])                  — enum with JSON-stringified values\n *   any of the above + .optional()      — optional modifier\n */\nfunction isSafeZodType(expr: string): boolean {\n  const base = expr.replace(/\\.optional\\(\\)$/, '');\n  // Simple: z.string(), z.number(), z.unknown(), etc.\n  if (/^z\\.[a-z]+\\(\\)$/.test(base)) return true;\n  // Wrapper: z.array(z.string()), z.record(z.string(), z.number())\n  if (/^z\\.[a-z]+\\(z\\.[a-z]+\\(\\)(, z\\.[a-z]+\\(\\))?\\)$/.test(base)) return true;\n  // Enum: z.enum([\"a\", \"b\", \"c\"]) — values are JSON.stringify'd (no unescaped quotes/backslashes)\n  if (/^z\\.enum\\(\\[(\"[^\"\\\\]*\"(, \"[^\"\\\\]*\")*)\\]\\)$/.test(base)) return true;\n  return false;\n}\n\n/**\n * Map a TypeScript type annotation string to a Zod type expression.\n */\nfunction tsTypeToZodType(tsType: string | undefined): string {\n  if (!tsType) return 'z.unknown()';\n  switch (tsType) {\n    case 'string': return 'z.string()';\n    case 'number': return 'z.number()';\n    case 'boolean': return 'z.boolean()';\n    case 'Date': return 'z.date()';\n    case 'bigint': return 'z.bigint()';\n    case 'void': return 'z.void()';\n    case 'undefined': return 'z.undefined()';\n    case 'null': return 'z.null()';\n    case 'any': return 'z.any()';\n    case 'unknown': return 'z.unknown()';\n    case 'never': return 'z.never()';\n    default:\n      if (tsType.endsWith('[]')) {\n        const inner = tsTypeToZodType(tsType.slice(0, -2));\n        return `z.array(${inner})`;\n      }\n      if (tsType.startsWith('Record<')) {\n        const match = tsType.match(/^Record<(.+),\\s*(.+)>$/);\n        if (match) {\n          return `z.record(${tsTypeToZodType(match[1])}, ${tsTypeToZodType(match[2])})`;\n        }\n      }\n      return 'z.unknown()';\n  }\n}\n\n/**\n * Map a JSON Schema type string to a Zod type expression.\n */\nfunction jsonSchemaTypeToZodType(schemaType: string | undefined): string {\n  switch (schemaType) {\n    case 'string': return 'z.string()';\n    case 'number': case 'integer': return 'z.number()';\n    case 'boolean': return 'z.boolean()';\n    case 'array': return 'z.array(z.unknown())';\n    case 'object': return 'z.record(z.string(), z.unknown())';\n    case 'null': return 'z.null()';\n    default: return 'z.unknown()';\n  }\n}\n\n/**\n * Escape sourcePath to prevent comment injection (close-comment sequence).\n */\nexport function escapeSourcePath(path: string): string {\n  return path.replace(/\\*\\//g, '*\\\\/');\n}\n\n/**\n * Extract atom from Claude Code skill.\n */\nasync function extractFromSkill(skillPath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(skillPath, process.cwd());\n\n  // Check if it's a directory or file\n  const stats = await stat(resolvedPath);\n  let skillContent: string;\n  let skillFile: string;\n\n  if (stats.isDirectory()) {\n    // Look for SKILL.md in directory\n    skillFile = join(resolvedPath, 'SKILL.md');\n    if (!(await fileExists(skillFile))) {\n      throw new Error(`No SKILL.md found in ${resolvedPath}`);\n    }\n    skillContent = await readFile(skillFile, 'utf-8');\n  } else {\n    // Direct file path\n    skillFile = resolvedPath;\n    skillContent = await readFile(skillFile, 'utf-8');\n  }\n\n  // Parse frontmatter\n  const frontmatter = parseFrontmatter(skillContent);\n  const name = frontmatter['name'] || basename(dirname(skillFile));\n  const description = frontmatter['description'] || 'Extracted from Claude Code skill';\n\n  // Analyze content for input/output patterns\n  const inputFields = analyzeSkillInputs(skillContent);\n  const outputFields = analyzeSkillOutputs(skillContent);\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields,\n    outputFields,\n    sourceType: 'skill',\n    sourcePath: skillFile,\n  };\n}\n\n/**\n * Analyze content for field patterns matching a set of regexes.\n * Shared logic for input/output field extraction from skill documentation.\n */\nfunction analyzeFieldPatterns(\n  content: string,\n  patterns: RegExp[],\n  defaultField: { name: string; description: string },\n  descriptionSuffix: string,\n): ExtractedAtom['inputFields'] {\n  const found = new Set<string>();\n\n  for (const pattern of patterns) {\n    for (const match of content.matchAll(pattern)) {\n      const name = match[1]?.toLowerCase();\n      if (name && !found.has(name) && name.length > 2) {\n        found.add(name);\n      }\n    }\n  }\n\n  if (found.size === 0) {\n    return [{ name: defaultField.name, type: 'string', zodType: 'z.string()', description: defaultField.description }];\n  }\n\n  const fields: ExtractedAtom['inputFields'] = [];\n  for (const name of found) {\n    fields.push({ name: toSnakeCase(name), type: 'string', zodType: 'z.string()', description: `${name} ${descriptionSuffix}` });\n  }\n  return fields.slice(0, 5);\n}\n\nconst INPUT_PATTERNS = [\n  /accepts?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /input[:\\s]+([a-z_]+)/gi,\n  /receives?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /takes?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n];\n\nconst OUTPUT_PATTERNS = [\n  /outputs?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /returns?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /produces?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /generates?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n];\n\nfunction analyzeSkillInputs(content: string): ExtractedAtom['inputFields'] {\n  return analyzeFieldPatterns(content, INPUT_PATTERNS, { name: 'input', description: 'Input data to process' }, 'parameter');\n}\n\nfunction analyzeSkillOutputs(content: string): ExtractedAtom['outputFields'] {\n  return analyzeFieldPatterns(content, OUTPUT_PATTERNS, { name: 'result', description: 'Processing result' }, 'output');\n}\n\n/**\n * Extract atom from BMAD workflow.\n */\nasync function extractFromBmad(bmadPath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(bmadPath, process.cwd());\n\n  if (!(await fileExists(resolvedPath))) {\n    throw new Error(`BMAD workflow not found: ${resolvedPath}`);\n  }\n\n  const content = await readFile(resolvedPath, 'utf-8');\n  const frontmatter = parseFrontmatter(content);\n\n  const name = frontmatter['name'] || basename(resolvedPath, '.md');\n  const description = frontmatter['description'] || 'Extracted from BMAD workflow';\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields: [{ name: 'context', type: 'string', zodType: 'z.string()', description: 'Workflow context' }],\n    outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Workflow result' }],\n    sourceType: 'bmad',\n    sourcePath: resolvedPath,\n  };\n}\n\n/**\n * Extract atom from MCP tool definition.\n */\nasync function extractFromMcp(mcpPath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(mcpPath, process.cwd());\n\n  if (!(await fileExists(resolvedPath))) {\n    throw new Error(`MCP tool definition not found: ${resolvedPath}`);\n  }\n\n  const content = await readFile(resolvedPath, 'utf-8');\n\n  // Try to parse as JSON (MCP tool definitions are often JSON)\n  let mcpDef: { name?: string; description?: string; inputSchema?: unknown };\n  try {\n    mcpDef = JSON.parse(content);\n  } catch (err) {\n    // If not JSON, warn and treat as a generic definition\n    console.warn(\n      fmt.yellow(`Warning: Could not parse MCP definition as JSON: ${toErrorMessage(err)}`)\n    );\n    mcpDef = { name: basename(resolvedPath, '.json') };\n  }\n\n  const name = mcpDef.name || basename(resolvedPath, '.json');\n  const description = mcpDef.description || 'Extracted from MCP tool';\n\n  // Extract input fields from inputSchema if present\n  const inputFields: ExtractedAtom['inputFields'] = [];\n  if (mcpDef.inputSchema && typeof mcpDef.inputSchema === 'object') {\n    const schema = mcpDef.inputSchema as {\n      properties?: Record<string, { type?: string; description?: string; enum?: string[] }>;\n      required?: string[];\n    };\n    const required = new Set(schema.required ?? []);\n    if (schema.properties) {\n      for (const [key, value] of Object.entries(schema.properties)) {\n        let zodType: string;\n        if (value.enum) {\n          zodType = `z.enum([${value.enum.map(v => JSON.stringify(v)).join(', ')}])`;\n        } else {\n          zodType = jsonSchemaTypeToZodType(value.type);\n        }\n        if (!required.has(key)) {\n          zodType += '.optional()';\n        }\n        inputFields.push({\n          name: toSnakeCase(key),\n          type: value.type ?? 'unknown',\n          zodType,\n          description: value.description || `${key} parameter`,\n        });\n      }\n    }\n  }\n\n  if (inputFields.length === 0) {\n    inputFields.push({ name: 'input', type: 'string', zodType: 'z.string()', description: 'Tool input' });\n  }\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields,\n    outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Tool result' }],\n    sourceType: 'mcp',\n    sourcePath: resolvedPath,\n  };\n}\n\n/**\n * Extract atom from existing code file using AST-based extraction.\n *\n * For JS/TS files, uses oxc-parser via dynamic import to extract typed\n * function signatures. Falls back to regex for non-JS/TS or parse failures.\n * The dynamic import ensures oxc-parser is only loaded when --code is used.\n */\nasync function extractFromCode(codePath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(codePath, process.cwd());\n\n  if (!(await fileExists(resolvedPath))) {\n    throw new Error(`Code file not found: ${resolvedPath}`);\n  }\n\n  const content = await readFile(resolvedPath, 'utf-8');\n  const name = basename(resolvedPath).replace(/\\.[^.]+$/, '');\n\n  // Extract description from JSDoc or first comment\n  let description = 'Extracted from code';\n  const jsdocMatch = content.match(/\\/\\*\\*\\s*\\n\\s*\\*\\s*([^\\n]+)/);\n  if (jsdocMatch && jsdocMatch[1]) {\n    description = jsdocMatch[1].trim();\n  }\n\n  // Try AST-based extraction for JS/TS files\n  const { detectLanguage, isJavaScriptFamily, parseFile } = await import('../parser/index.js');\n  const { extractSignatures } = await import('../parser/signatures.js');\n  const lang = detectLanguage(resolvedPath);\n  const jsFamily = lang && isJavaScriptFamily(lang);\n\n  if (jsFamily) {\n    try {\n\n      const parseResult = await parseFile(content, resolvedPath);\n      if (parseResult.success && parseResult.language !== 'python') {\n        const sigs = extractSignatures(parseResult.ast, content, parseResult.comments);\n        // Pick primary export: first default export, or first named export\n        const primary = sigs.find(s => s.exportDefault) ?? sigs.find(s => s.exported) ?? sigs[0];\n\n        if (primary) {\n          const inputFields: ExtractedAtom['inputFields'] = primary.params\n            .filter(p => {\n              const fieldName = toSnakeCase(p.name);\n              return VALID_JS_IDENTIFIER.test(fieldName);\n            })\n            .map(p => ({\n              name: toSnakeCase(p.name),\n              type: p.type ?? 'unknown',\n              zodType: tsTypeToZodType(p.type),\n              description: `${p.name} parameter`,\n            }));\n\n          if (inputFields.length === 0) {\n            inputFields.push({ name: 'input', type: 'unknown', zodType: 'z.unknown()', description: 'Function input' });\n          }\n\n          return {\n            name: toSnakeCase(name),\n            description,\n            inputFields,\n            outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Function result' }],\n            sourceType: 'code',\n            sourcePath: resolvedPath,\n          };\n        }\n      }\n      // Parse succeeded but no functions found — fall through to regex\n    } catch {\n      // AST parse failed — fall through to regex fallback\n    }\n  }\n\n  // Regex fallback for non-JS/TS files or parse failures\n  const inputFields: ExtractedAtom['inputFields'] = [];\n  const functionMatch = content.match(/(?:function|const|let|var)\\s+\\w+\\s*[=:]\\s*(?:async\\s+)?(?:\\([^)]*\\)|[^=]+=>)/);\n  if (functionMatch && functionMatch[0]) {\n    const paramMatch = functionMatch[0].match(/\\(([^)]*)\\)/);\n    if (paramMatch && paramMatch[1]) {\n      const paramsStr = paramMatch[1];\n      const params = paramsStr.split(',').map((p) => p.trim().split(':')[0]?.trim() ?? '');\n      for (const param of params) {\n        if (param && param !== '' && !param.startsWith('{')) {\n          inputFields.push({\n            name: toSnakeCase(param),\n            type: 'string',\n            zodType: 'z.string()',\n            description: `${param} parameter`,\n          });\n        }\n      }\n    }\n  }\n\n  if (inputFields.length === 0) {\n    inputFields.push({ name: 'input', type: 'string', zodType: 'z.string()', description: 'Function input' });\n  }\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields,\n    outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Function result' }],\n    sourceType: 'code',\n    sourcePath: resolvedPath,\n  };\n}\n\n/**\n * Escape a string for use in a single-quoted TypeScript string literal.\n */\nfunction escapeForTemplate(str: string): string {\n  return str\n    .replace(/\\\\/g, '\\\\\\\\')\n    .replace(/'/g, \"\\\\'\")\n    .replace(/`/g, '\\\\`')\n    .replace(/\\$\\{/g, '\\\\${')\n    .replace(/\\*\\//g, '* /')\n    .replace(/\\n/g, ' ')\n    .replace(/\\r/g, '');\n}\n\n/**\n * Generate atom template from extracted definition.\n */\nfunction generateAtomTemplate(extracted: ExtractedAtom): string {\n  const escapedName = escapeForTemplate(extracted.name);\n  const escapedDescription = escapeForTemplate(extracted.description);\n  const escapedPath = escapeSourcePath(extracted.sourcePath);\n\n  // Filter fields to valid JS identifiers and safe Zod types only\n  const safeInputFields = extracted.inputFields\n    .filter(f => VALID_JS_IDENTIFIER.test(f.name) && isSafeZodType(f.zodType));\n  const safeOutputFields = extracted.outputFields\n    .filter(f => VALID_JS_IDENTIFIER.test(f.name) && isSafeZodType(f.zodType));\n\n  const droppedInputCount = extracted.inputFields.length - safeInputFields.length;\n  const droppedOutputCount = extracted.outputFields.length - safeOutputFields.length;\n  if (droppedInputCount > 0 || droppedOutputCount > 0) {\n    const parts: string[] = [];\n    if (droppedInputCount > 0) parts.push(`${droppedInputCount} input`);\n    if (droppedOutputCount > 0) parts.push(`${droppedOutputCount} output`);\n    console.error(fmt.warning(`Dropped ${parts.join(' and ')} field(s) with unsafe or invalid schema types`));\n  }\n\n  const inputSchema = safeInputFields\n    .map((f) => `    ${f.name}: ${f.zodType}.describe('${escapeForTemplate(f.description)}'),`)\n    .join('\\n');\n\n  const outputSchema = safeOutputFields\n    .map((f) => `    ${f.name}: ${f.zodType}.describe('${escapeForTemplate(f.description)}'),`)\n    .join('\\n');\n\n  const inputDestructure = safeInputFields.map((f) => f.name).join(', ');\n\n  return `import { defineAtom, success, executionError, z } from 'atomism';\n\n/**\n * ${escapedName} atom\n *\n * ${escapeForTemplate(extracted.description)}\n *\n * Extracted from: ${extracted.sourceType} at ${escapedPath}\n */\nexport default defineAtom({\n  name: '${escapedName}',\n  description: '${escapedDescription}',\n  input: z.object({\n${inputSchema}\n  }),\n  output: z.object({\n${outputSchema}\n  }),\n  tests: {\n    path: './${escapedName}.test.ts',\n  },\n  idempotent: true,\n  handler: async ({ ${inputDestructure} }) => {\n    // TODO: Implement handler logic\n    // Original source: ${escapedPath}\n\n    return success({\n${safeOutputFields.map((f) => `      ${f.name}: '',`).join('\\n')}\n    });\n  },\n});\n`;\n}\n\n/**\n * Generate test template from extracted definition.\n */\nfunction generateTestTemplate(extracted: ExtractedAtom): string {\n  const escapedName = escapeForTemplate(extracted.name);\n  const safeInputFields = extracted.inputFields.filter(f => VALID_JS_IDENTIFIER.test(f.name));\n  return `import { describe, it, expect } from 'vitest';\nimport atom from './${escapedName}.js';\n\ndescribe('${escapedName}', () => {\n  describe('input validation', () => {\n${safeInputFields.map((f) => `    it.todo('validates ${f.name} field');`).join('\\n')}\n  });\n\n  describe('handler behavior', () => {\n    it.todo('processes valid input correctly');\n    it.todo('returns expected output structure');\n  });\n\n  describe('error handling', () => {\n    it.todo('handles invalid input gracefully');\n  });\n});\n`;\n}\n\n/**\n * Format extracted definition for display.\n */\nfunction formatExtractedAtom(extracted: ExtractedAtom): string {\n  const lines: string[] = [];\n\n  lines.push(fmt.bold('Proposed Atom Definition'));\n  lines.push('─'.repeat(60));\n  lines.push(`  ${fmt.dim('Name:')}        ${fmt.cyan(extracted.name)}`);\n  lines.push(`  ${fmt.dim('Source:')}      ${extracted.sourceType} (${extracted.sourcePath})`);\n  lines.push(`  ${fmt.dim('Description:')} ${extracted.description.substring(0, 60)}${extracted.description.length > 60 ? 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Run: atomic register ${atomPath}`);\n    }\n  } catch (err) {\n    const message = toErrorMessage(err);\n    if (options.json) {\n      const { deriveErrorCode } = await import('./helpers.js');\n      console.log(JSON.stringify({ success: false, error: message, errorCode: deriveErrorCode(err) }, null, 2));\n    } else {\n      console.error(fmt.error(`Extraction failed: ${message}`));\n    }\n    process.exit(1);\n  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'*\\\\/');\n}\n\n/**\n * Extract atom from Claude Code skill.\n */\nasync function extractFromSkill(skillPath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(skillPath, process.cwd());\n\n  // Check if it's a directory or file\n  const stats = await stat(resolvedPath);\n  let skillContent: string;\n  let skillFile: string;\n\n  if (stats.isDirectory()) {\n    // Look for SKILL.md in directory\n    skillFile = join(resolvedPath, 'SKILL.md');\n    if (!(await fileExists(skillFile))) {\n      throw new Error(`No SKILL.md found in ${resolvedPath}`);\n    }\n    skillContent = await readFile(skillFile, 'utf-8');\n  } else {\n    // Direct file path\n    skillFile = resolvedPath;\n    skillContent = await readFile(skillFile, 'utf-8');\n  }\n\n  // Parse frontmatter\n  const frontmatter = parseFrontmatter(skillContent);\n  const name = frontmatter['name'] || basename(dirname(skillFile));\n  const description = frontmatter['description'] || 'Extracted from Claude Code skill';\n\n  // Analyze content for input/output patterns\n  const inputFields = analyzeSkillInputs(skillContent);\n  const outputFields = analyzeSkillOutputs(skillContent);\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields,\n    outputFields,\n    sourceType: 'skill',\n    sourcePath: skillFile,\n  };\n}\n\n/**\n * Analyze content for field patterns matching a set of regexes.\n * Shared logic for input/output field extraction from skill documentation.\n */\nfunction analyzeFieldPatterns(\n  content: string,\n  patterns: RegExp[],\n  defaultField: { name: string; description: string },\n  descriptionSuffix: string,\n): ExtractedAtom['inputFields'] {\n  const found = new Set<string>();\n\n  for (const pattern of patterns) {\n    for (const match of content.matchAll(pattern)) {\n      const name = match[1]?.toLowerCase();\n      if (name && !found.has(name) && name.length > 2) {\n        found.add(name);\n      }\n    }\n  }\n\n  if (found.size === 0) {\n    return [{ name: defaultField.name, type: 'string', zodType: 'z.string()', description: defaultField.description }];\n  }\n\n  const fields: ExtractedAtom['inputFields'] = [];\n  for (const name of found) {\n    fields.push({ name: toSnakeCase(name), type: 'string', zodType: 'z.string()', description: `${name} ${descriptionSuffix}` });\n  }\n  return fields.slice(0, 5);\n}\n\nconst INPUT_PATTERNS = [\n  /accepts?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /input[:\\s]+([a-z_]+)/gi,\n  /receives?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /takes?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n];\n\nconst OUTPUT_PATTERNS = [\n  /outputs?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /returns?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /produces?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n  /generates?\\s+(?:an?\\s+)?([a-z_]+)/gi,\n];\n\nfunction analyzeSkillInputs(content: string): ExtractedAtom['inputFields'] {\n  return analyzeFieldPatterns(content, INPUT_PATTERNS, { name: 'input', description: 'Input data to process' }, 'parameter');\n}\n\nfunction analyzeSkillOutputs(content: string): ExtractedAtom['outputFields'] {\n  return analyzeFieldPatterns(content, OUTPUT_PATTERNS, { name: 'result', description: 'Processing result' }, 'output');\n}\n\n/**\n * Extract atom from BMAD workflow.\n */\nasync function extractFromBmad(bmadPath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(bmadPath, process.cwd());\n\n  if (!(await fileExists(resolvedPath))) {\n    throw new Error(`BMAD workflow not found: ${resolvedPath}`);\n  }\n\n  const content = await readFile(resolvedPath, 'utf-8');\n  const frontmatter = parseFrontmatter(content);\n\n  const name = frontmatter['name'] || basename(resolvedPath, '.md');\n  const description = frontmatter['description'] || 'Extracted from BMAD workflow';\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields: [{ name: 'context', type: 'string', zodType: 'z.string()', description: 'Workflow context' }],\n    outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Workflow result' }],\n    sourceType: 'bmad',\n    sourcePath: resolvedPath,\n  };\n}\n\n/**\n * Extract atom from MCP tool definition.\n */\nasync function extractFromMcp(mcpPath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(mcpPath, process.cwd());\n\n  if (!(await fileExists(resolvedPath))) {\n    throw new Error(`MCP tool definition not found: ${resolvedPath}`);\n  }\n\n  const content = await readFile(resolvedPath, 'utf-8');\n\n  // Try to parse as JSON (MCP tool definitions are often JSON)\n  let mcpDef: { name?: string; description?: string; inputSchema?: unknown };\n  try {\n    mcpDef = JSON.parse(content);\n  } catch (err) {\n    // If not JSON, warn and treat as a generic definition\n    console.warn(\n      fmt.yellow(`Warning: Could not parse MCP definition as JSON: ${toErrorMessage(err)}`)\n    );\n    mcpDef = { name: basename(resolvedPath, '.json') };\n  }\n\n  const name = mcpDef.name || basename(resolvedPath, '.json');\n  const description = mcpDef.description || 'Extracted from MCP tool';\n\n  // Extract input fields from inputSchema if present\n  const inputFields: ExtractedAtom['inputFields'] = [];\n  if (mcpDef.inputSchema && typeof mcpDef.inputSchema === 'object') {\n    const schema = mcpDef.inputSchema as {\n      properties?: Record<string, { type?: string; description?: string; enum?: string[] }>;\n      required?: string[];\n    };\n    const required = new Set(schema.required ?? []);\n    if (schema.properties) {\n      for (const [key, value] of Object.entries(schema.properties)) {\n        let zodType: string;\n        if (value.enum) {\n          zodType = `z.enum([${value.enum.map(v => JSON.stringify(v)).join(', ')}])`;\n        } else {\n          zodType = jsonSchemaTypeToZodType(value.type);\n        }\n        if (!required.has(key)) {\n          zodType += '.optional()';\n        }\n        inputFields.push({\n          name: toSnakeCase(key),\n          type: value.type ?? 'unknown',\n          zodType,\n          description: value.description || `${key} parameter`,\n        });\n      }\n    }\n  }\n\n  if (inputFields.length === 0) {\n    inputFields.push({ name: 'input', type: 'string', zodType: 'z.string()', description: 'Tool input' });\n  }\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields,\n    outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Tool result' }],\n    sourceType: 'mcp',\n    sourcePath: resolvedPath,\n  };\n}\n\n/**\n * Extract atom from existing code file using AST-based extraction.\n *\n * For JS/TS files, uses oxc-parser via dynamic import to extract typed\n * function signatures. Falls back to regex for non-JS/TS or parse failures.\n * The dynamic import ensures oxc-parser is only loaded when --code is used.\n */\nasync function extractFromCode(codePath: string): Promise<ExtractedAtom> {\n  const resolvedPath = resolveAtomPath(codePath, process.cwd());\n\n  if (!(await fileExists(resolvedPath))) {\n    throw new Error(`Code file not found: ${resolvedPath}`);\n  }\n\n  const content = await readFile(resolvedPath, 'utf-8');\n  const name = basename(resolvedPath).replace(/\\.[^.]+$/, '');\n\n  // Extract description from JSDoc or first comment\n  let description = 'Extracted from code';\n  const jsdocMatch = content.match(/\\/\\*\\*\\s*\\n\\s*\\*\\s*([^\\n]+)/);\n  if (jsdocMatch && jsdocMatch[1]) {\n    description = jsdocMatch[1].trim();\n  }\n\n  // Try AST-based extraction for JS/TS files\n  const { detectLanguage, isJavaScriptFamily, parseFile } = await import('../parser/index.js');\n  const { extractSignatures } = await import('../parser/signatures.js');\n  const lang = detectLanguage(resolvedPath);\n  const jsFamily = lang && isJavaScriptFamily(lang);\n\n  if (jsFamily) {\n    try {\n\n      const parseResult = await parseFile(content, resolvedPath);\n      if (parseResult.success && parseResult.language !== 'python') {\n        const sigs = extractSignatures(parseResult.ast, content, parseResult.comments);\n        // Pick primary export: first default export, or first named export\n        const primary = sigs.find(s => s.exportDefault) ?? sigs.find(s => s.exported) ?? sigs[0];\n\n        if (primary) {\n          const inputFields: ExtractedAtom['inputFields'] = primary.params\n            .filter(p => {\n              const fieldName = toSnakeCase(p.name);\n              return VALID_JS_IDENTIFIER.test(fieldName);\n            })\n            .map(p => ({\n              name: toSnakeCase(p.name),\n              type: p.type ?? 'unknown',\n              zodType: tsTypeToZodType(p.type),\n              description: `${p.name} parameter`,\n            }));\n\n          if (inputFields.length === 0) {\n            inputFields.push({ name: 'input', type: 'unknown', zodType: 'z.unknown()', description: 'Function input' });\n          }\n\n          return {\n            name: toSnakeCase(name),\n            description,\n            inputFields,\n            outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Function result' }],\n            sourceType: 'code',\n            sourcePath: resolvedPath,\n          };\n        }\n      }\n      // Parse succeeded but no functions found — fall through to regex\n    } catch {\n      // AST parse failed — fall through to regex fallback\n    }\n  }\n\n  // Regex fallback for non-JS/TS files or parse failures\n  const inputFields: ExtractedAtom['inputFields'] = [];\n  const functionMatch = content.match(/(?:function|const|let|var)\\s+\\w+\\s*[=:]\\s*(?:async\\s+)?(?:\\([^)]*\\)|[^=]+=>)/);\n  if (functionMatch && functionMatch[0]) {\n    const paramMatch = functionMatch[0].match(/\\(([^)]*)\\)/);\n    if (paramMatch && paramMatch[1]) {\n      const paramsStr = paramMatch[1];\n      const params = paramsStr.split(',').map((p) => p.trim().split(':')[0]?.trim() ?? '');\n      for (const param of params) {\n        if (param && param !== '' && !param.startsWith('{')) {\n          inputFields.push({\n            name: toSnakeCase(param),\n            type: 'string',\n            zodType: 'z.string()',\n            description: `${param} parameter`,\n          });\n        }\n      }\n    }\n  }\n\n  if (inputFields.length === 0) {\n    inputFields.push({ name: 'input', type: 'string', zodType: 'z.string()', description: 'Function input' });\n  }\n\n  return {\n    name: toSnakeCase(name),\n    description,\n    inputFields,\n    outputFields: [{ name: 'result', type: 'string', zodType: 'z.string()', description: 'Function result' }],\n    sourceType: 'code',\n    sourcePath: resolvedPath,\n  };\n}\n\n/**\n * Escape a string for use in a single-quoted TypeScript string literal.\n */\nfunction escapeForTemplate(str: string): string {\n  return str\n    .replace(/\\\\/g, '\\\\\\\\')\n    .replace(/'/g, \"\\\\'\")\n    .replace(/`/g, '\\\\`')\n    .replace(/\\$\\{/g, '\\\\${')\n    .replace(/\\*\\//g, '* /')\n    .replace(/\\n/g, ' ')\n    .replace(/\\r/g, '');\n}\n\n/**\n * Generate atom template from extracted definition.\n */\nfunction generateAtomTemplate(extracted: ExtractedAtom): string {\n  const escapedName = escapeForTemplate(extracted.name);\n  const escapedDescription = escapeForTemplate(extracted.description);\n  const escapedPath = escapeSourcePath(extracted.sourcePath);\n\n  // Filter fields to valid JS identifiers and safe Zod types only\n  const safeInputFields = extracted.inputFields\n    .filter(f => VALID_JS_IDENTIFIER.test(f.name) && isSafeZodType(f.zodType));\n  const safeOutputFields = extracted.outputFields\n    .filter(f => VALID_JS_IDENTIFIER.test(f.name) && isSafeZodType(f.zodType));\n\n  const droppedInputCount = extracted.inputFields.length - safeInputFields.length;\n  const droppedOutputCount = extracted.outputFields.length - safeOutputFields.length;\n  if (droppedInputCount > 0 || droppedOutputCount > 0) {\n    const parts: string[] = [];\n    if (droppedInputCount > 0) parts.push(`${droppedInputCount} input`);\n    if (droppedOutputCount > 0) parts.push(`${droppedOutputCount} output`);\n    console.error(fmt.warning(`Dropped ${parts.join(' and ')} field(s) with unsafe or invalid schema types`));\n  }\n\n  const inputSchema = safeInputFields\n    .map((f) => `    ${f.name}: ${f.zodType}.describe('${escapeForTemplate(f.description)}'),`)\n    .join('\\n');\n\n  const outputSchema = safeOutputFields\n    .map((f) => `    ${f.name}: ${f.zodType}.describe('${escapeForTemplate(f.description)}'),`)\n    .join('\\n');\n\n  const inputDestructure = safeInputFields.map((f) => f.name).join(', ');\n\n  return `import { defineAtom, success, executionError, z } from 'atomism';\n\n/**\n * ${escapedName} atom\n *\n * ${escapeForTemplate(extracted.description)}\n *\n * Extracted from: ${extracted.sourceType} at ${escapedPath}\n */\nexport default defineAtom({\n  name: '${escapedName}',\n  description: '${escapedDescription}',\n  input: z.object({\n${inputSchema}\n  }),\n  output: z.object({\n${outputSchema}\n  }),\n  tests: {\n    path: './${escapedName}.test.ts',\n  },\n  idempotent: true,\n  handler: async ({ ${inputDestructure} }) => {\n    // TODO: Implement handler logic\n    // Original source: ${escapedPath}\n\n    return success({\n${safeOutputFields.map((f) => `      ${f.name}: '',`).join('\\n')}\n    });\n  },\n});\n`;\n}\n\n/**\n * Generate test template from extracted definition.\n */\nfunction generateTestTemplate(extracted: ExtractedAtom): string {\n  const escapedName = escapeForTemplate(extracted.name);\n  const safeInputFields = extracted.inputFields.filter(f => VALID_JS_IDENTIFIER.test(f.name));\n  return `import { describe, it, expect } from 'vitest';\nimport atom from './${escapedName}.js';\n\ndescribe('${escapedName}', () => {\n  describe('input validation', () => {\n${safeInputFields.map((f) => `    it.todo('validates ${f.name} field');`).join('\\n')}\n  });\n\n  describe('handler behavior', () => {\n    it.todo('processes valid input correctly');\n    it.todo('returns expected output structure');\n  });\n\n  describe('error handling', () => {\n    it.todo('handles invalid input gracefully');\n  });\n});\n`;\n}\n\n/**\n * Format extracted definition for display.\n */\nfunction formatExtractedAtom(extracted: ExtractedAtom): string {\n  const lines: string[] = [];\n\n  lines.push(fmt.bold('Proposed Atom Definition'));\n  lines.push('─'.repeat(60));\n  lines.push(`  ${fmt.dim('Name:')}        ${fmt.cyan(extracted.name)}`);\n  lines.push(`  ${fmt.dim('Source:')}      ${extracted.sourceType} (${extracted.sourcePath})`);\n  lines.push(`  ${fmt.dim('Description:')} ${extracted.description.substring(0, 60)}${extracted.description.length > 60 ? '...' : ''}`);\n  lines.push('');\n\n  lines.push(fmt.bold('Input Schema'));\n  lines.push('─'.repeat(60));\n  for (const field of extracted.inputFields) {\n    lines.push(`  ${fmt.green(field.name)}: ${field.type}`);\n    lines.push(`    ${fmt.dim(field.description)}`);\n  }\n  lines.push('');\n\n  lines.push(fmt.bold('Output Schema'));\n  lines.push('─'.repeat(60));\n  for (const field of extracted.outputFields) {\n    lines.push(`  ${fmt.green(field.name)}: ${field.type}`);\n    lines.push(`    ${fmt.dim(field.description)}`);\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Extract command handler.\n */\nexport async function extractCommand(options: ExtractOptions): Promise<void> {\n  const projectRoot = process.cwd();\n\n  try {\n    // Determine source type and path\n    let extracted: ExtractedAtom;\n\n    if (options.skill) {\n      extracted = await extractFromSkill(options.skill);\n    } else if (options.bmad) {\n      extracted = await extractFromBmad(options.bmad);\n    } else if (options.mcp) {\n      extracted = await extractFromMcp(options.mcp);\n    } else if (options.code) {\n      extracted = await extractFromCode(options.code);\n    } else {\n      throw new Error(\n        'No source specified.\\n' +\n          'Use one of: --skill <path>, --bmad <path>, --mcp <path>, --code <path>'\n      );\n    }\n\n    // Display proposed definition\n    if (!options.json) {\n      console.log(formatExtractedAtom(extracted));\n      console.log('');\n    }\n\n    // If --yes not specified and not in JSON mode, show preview and exit\n    if (!options.yes && !options.json) {\n      console.log(fmt.yellow('Use --yes to automatically create the atom.'));\n      console.log(fmt.dim('Use --json for programmatic output.'));\n      return;\n    }\n\n    // If --yes not specified but in JSON mode, output dry-run with wouldWriteTo\n    if (!options.yes && options.json) {\n      const outputDir = options.output\n        ? resolveAtomPath(options.output, projectRoot)\n        : join(projectRoot, 'atoms');\n      const result: ExtractResult & { wouldWriteTo?: { atom: string; test: string } } = {\n        success: true,\n        extracted,\n        wouldWriteTo: {\n          atom: join(outputDir, `${extracted.name}.ts`),\n          test: join(outputDir, `${extracted.name}.test.ts`),\n        },\n      };\n      console.log(JSON.stringify(result, null, 2));\n      return;\n    }\n\n    // Initialize storage if needed\n    const atomicPath = join(projectRoot, ATOMIC_DIR);\n    if (!(await fileExists(atomicPath))) {\n      await initStorage(projectRoot);\n    }\n\n    // Determine output directory\n    const outputDir = options.output\n      ? resolveAtomPath(options.output, projectRoot)\n      : join(projectRoot, 'atoms');\n\n    await mkdir(outputDir, { recursive: true });\n\n    // Check if files already exist (with path containment guard)\n    const atomPath = join(outputDir, `${extracted.name}.ts`);\n    const testPath = join(outputDir, `${extracted.name}.test.ts`);\n    const resolvedOutputDir = resolve(outputDir);\n    const rel = relative(resolvedOutputDir, resolve(atomPath));\n    if (isAbsolute(rel) || rel.startsWith('..')) {\n      throw new Error('Generated path escapes output directory');\n    }\n\n    if (await fileExists(atomPath)) {\n      throw new Error(`Atom file already exists: ${atomPath}`);\n    }\n    if (await fileExists(testPath)) {\n      throw new Error(`Test file already exists: ${testPath}`);\n    }\n\n    // Write files\n    await writeFile(atomPath, generateAtomTemplate(extracted));\n    await writeFile(testPath, generateTestTemplate(extracted));\n\n    // Output result\n    const result: ExtractResult = {\n      success: true,\n      extracted,\n      atomPath,\n      testPath,\n    };\n\n    if (options.json) {\n      console.log(JSON.stringify(result, null, 2));\n    } else {\n      console.log(fmt.green('✓ Atom extracted successfully'));\n      console.log(`  ${fmt.dim('Atom:')} ${atomPath}`);\n      console.log(`  ${fmt.dim('Test:')} ${testPath}`);\n      console.log('');\n      console.log('Next steps:');\n      console.log(`  1. Review and edit ${atomPath}`);\n      console.log(`  2. Run: atomic register ${atomPath}`);\n    }\n  } catch (err) {\n    const message = toErrorMessage(err);\n    if (options.json) {\n      const { deriveErrorCode } = await import('./helpers.js');\n      console.log(JSON.stringify({ success: false, error: message, errorCode: deriveErrorCode(err) }, null, 2));\n    } else {\n      console.error(fmt.error(`Extraction failed: ${message}`));\n    }\n    process.exit(1);\n  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package/dist/{init-2FINDMYK.js → init-EH6ZWP5R.js}

@@ -608,7 +608,8 @@ async function ensureDeps(projectRoot) {
   try {
     execSync(`node -e "require.resolve('atomism')"`, {
       cwd: projectRoot,
-      stdio: "ignore"
+      stdio: "ignore",
+      timeout: 5e3
     });
     return { success: true, packageJsonCreated, tsconfigCreated, tsconfigNeedsInclude, suggestedInclude, atomismLinked };
   } catch {
@@ -738,4 +739,4 @@ async function initCommand(options) {
 export {
   initCommand
 };
-//# sourceMappingURL=init-2FINDMYK.js.map
+//# sourceMappingURL=init-EH6ZWP5R.js.map

package/dist/init-EH6ZWP5R.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/commands/init.ts","../src/commands/skills-init.ts","../src/commands/claude-md-init.ts","../src/commands/gitignore-init.ts"],"sourcesContent":["import { readFile, writeFile, access } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { execSync } from 'node:child_process';\nimport { initStorage } from '../storage/index.js';\nimport { initSkill } from './skills-init.js';\nimport { initClaudeMd } from './claude-md-init.js';\nimport { initGitignore } from './gitignore-init.js';\nimport { toErrorMessage } from '../utils/errors.js';\nimport { withErrorHandling } from './helpers.js';\n\nexport interface InitOptions {\n  json?: boolean;\n}\n\ninterface DepsResult {\n  success: boolean;\n  packageJsonCreated: boolean;\n  tsconfigCreated: boolean;\n  tsconfigNeedsInclude?: boolean;\n  suggestedInclude?: string;\n  atomismLinked: boolean;\n  error?: string;\n}\n\n/**\n * Ensure the project can resolve 'atomism' and 'zod' as modules.\n *\n * Atoms are TypeScript files that import from 'atomism'. Without a local\n * package.json that resolves the module, `atomic register` and any TS\n * tooling will fail with \"Cannot find module 'atomism'\".\n */\nasync function ensureDeps(projectRoot: string): Promise<DepsResult> {\n  const pkgPath = join(projectRoot, 'package.json');\n  const tsconfigPath = join(projectRoot, 'tsconfig.json');\n  let packageJsonCreated = false;\n  let tsconfigCreated = false;\n  let atomismLinked = false;\n\n  // 1. Ensure package.json exists\n  let hasPackageJson = false;\n  try {\n    await access(pkgPath);\n    hasPackageJson = true;\n  } catch {\n    // No package.json — create a minimal one\n  }\n\n  if (!hasPackageJson) {\n    const minimal = {\n      private: true,\n      description: 'Atomism-enabled project',\n      dependencies: {},\n    };\n    await writeFile(pkgPath, JSON.stringify(minimal, null, 2) + '\\n');\n    packageJsonCreated = true;\n  }\n\n  // 2. Ensure tsconfig.json exists (required for TS type inference in atoms)\n  let hasTsconfig = false;\n  try {\n    await access(tsconfigPath);\n    hasTsconfig = true;\n  } catch {\n    // No tsconfig.json\n  }\n\n  let tsconfigNeedsInclude: boolean | undefined;\n  let suggestedInclude: string | undefined;\n\n  if (hasTsconfig) {\n    // Check if existing tsconfig includes atom files\n    try {\n      const raw = await readFile(tsconfigPath, 'utf-8');\n      const parsed = JSON.parse(raw);\n      const includes: string[] = Array.isArray(parsed.include) ? parsed.include : [];\n      const coversAtoms = includes.some((pattern: string) =>\n        pattern === 'atoms/**/*.ts' ||\n        pattern.startsWith('atoms/') ||\n        pattern === '**/*.ts' ||\n        pattern === './**/*.ts'\n      );\n      if (!coversAtoms) {\n        tsconfigNeedsInclude = true;\n        suggestedInclude = 'atoms/**/*.ts';\n      }\n    } catch {\n      // tsconfig parse failure is non-fatal — skip the check\n    }\n  } else {\n    const tsconfig = {\n      compilerOptions: {\n        target: 'ES2022',\n        module: 'ESNext',\n        moduleResolution: 'bundler',\n        strict: true,\n        esModuleInterop: true,\n        skipLibCheck: true,\n        outDir: 'dist',\n      },\n      include: ['atoms/**/*.ts'],\n    };\n    await writeFile(tsconfigPath, JSON.stringify(tsconfig, null, 2) + '\\n');\n    tsconfigCreated = true;\n  }\n\n  // 3. Check if atomism is resolvable\n  try {\n    execSync('node -e \"require.resolve(\\'atomism\\')\"', {\n      cwd: projectRoot,\n      stdio: 'ignore',\n      timeout: 5000,\n    });\n    // Already resolvable\n    return { success: true, packageJsonCreated, tsconfigCreated, tsconfigNeedsInclude, suggestedInclude, atomismLinked };\n  } catch {\n    // Not resolvable — try to link it\n  }\n\n  // 4. Link atomism (works when atomism is installed globally via npm link)\n  try {\n    execSync('npm link atomism', {\n      cwd: projectRoot,\n      stdio: 'ignore',\n      timeout: 30000,\n    });\n    atomismLinked = true;\n  } catch {\n    return {\n      success: false,\n      packageJsonCreated,\n      tsconfigCreated,\n      tsconfigNeedsInclude,\n      suggestedInclude,\n      atomismLinked: false,\n      error: 'Could not resolve atomism. Run: npm link atomism (if globally installed) or npm install atomism',\n    };\n  }\n\n  return { success: true, packageJsonCreated, tsconfigCreated, tsconfigNeedsInclude, suggestedInclude, atomismLinked };\n}\n\nexport async function initCommand(options: InitOptions): Promise<void> {\n  await withErrorHandling(options, async () => {\n    const projectRoot = process.cwd();\n    const result = await initStorage(projectRoot);\n\n    // Ensure module resolution (non-fatal — warn but continue)\n    let depsResult: DepsResult;\n    try {\n      depsResult = await ensureDeps(projectRoot);\n    } catch (depsError) {\n      depsResult = {\n        success: false,\n        packageJsonCreated: false,\n        tsconfigCreated: false,\n        atomismLinked: false,\n        error: toErrorMessage(depsError),\n      };\n    }\n\n    // Create Claude Code skill (non-fatal)\n    let skillResult: { success: boolean; skipped?: boolean; path?: string; error?: string };\n    try {\n      skillResult = await initSkill({ force: false });\n    } catch (skillError) {\n      skillResult = {\n        success: false,\n        error: toErrorMessage(skillError),\n      };\n    }\n\n    // Create CLAUDE.md snippet (non-fatal)\n    let claudeMdResult: { success: boolean; skipped?: boolean; path?: string; error?: string };\n    try {\n      claudeMdResult = await initClaudeMd();\n    } catch (claudeError) {\n      claudeMdResult = {\n        success: false,\n        error: toErrorMessage(claudeError),\n      };\n    }\n\n    // Manage .gitignore (non-fatal)\n    let gitignoreResult: { success: boolean; skipped?: boolean; path?: string; error?: string };\n    try {\n      gitignoreResult = await initGitignore(projectRoot);\n    } catch (gitignoreError) {\n      gitignoreResult = {\n        success: false,\n        error: toErrorMessage(gitignoreError),\n      };\n    }\n\n    if (options.json) {\n      console.log(JSON.stringify({\n        ...result,\n        deps: depsResult,\n        skill: skillResult,\n        claudeMd: claudeMdResult,\n        gitignore: gitignoreResult,\n      }, null, 2));\n    } else {\n      if (result.created) {\n        console.log(`✓ Created ${result.path}`);\n      } else {\n        console.log(`✓ ${result.path} already exists`);\n      }\n      console.log(`✓ Database initialized at ${result.dbPath}`);\n      console.log(`✓ ${result.migrationsRun} migrations applied`);\n\n      // Report deps status\n      if (depsResult.success) {\n        if (depsResult.packageJsonCreated) {\n          console.log('✓ Created package.json for module resolution');\n        }\n        if (depsResult.tsconfigCreated) {\n          console.log('✓ Created tsconfig.json for atom type inference');\n        }\n        if (depsResult.atomismLinked) {\n          console.log('✓ Linked atomism for module resolution');\n        }\n      } else {\n        console.log(`⚠ Module resolution: ${depsResult.error ?? 'unknown error'}`);\n      }\n\n      // tsconfig warning is useful regardless of deps success\n      if (depsResult.tsconfigNeedsInclude) {\n        console.log(`⚠ tsconfig.json does not include atom files. Add to your \"include\" array:`);\n        console.log(`  \"${depsResult.suggestedInclude}\"`);\n      }\n\n      // Report skill status\n      if (skillResult.success && !skillResult.skipped) {\n        console.log(`✓ Claude Code skill created at ${skillResult.path}`);\n      } else if (skillResult.skipped) {\n        console.log('✓ Claude Code skill already exists');\n      } else if (!skillResult.success) {\n        console.log(`⚠ Claude Code skill creation failed: ${skillResult.error ?? 'unknown error'}`);\n      }\n\n      // Report CLAUDE.md status\n      if (claudeMdResult.success && !claudeMdResult.skipped) {\n        console.log(`✓ CLAUDE.md updated at ${claudeMdResult.path}`);\n      } else if (claudeMdResult.skipped) {\n        console.log('✓ CLAUDE.md already has atomism section');\n      } else if (!claudeMdResult.success) {\n        console.log(`⚠ CLAUDE.md update failed: ${claudeMdResult.error ?? 'unknown error'}`);\n      }\n\n      // Report .gitignore status\n      if (gitignoreResult.success && !gitignoreResult.skipped) {\n        console.log(`✓ .gitignore updated at ${gitignoreResult.path}`);\n      } else if (gitignoreResult.skipped) {\n        console.log('✓ .gitignore already has atomism entries');\n      } else if (!gitignoreResult.success) {\n        console.log(`⚠ .gitignore update failed: ${gitignoreResult.error ?? 'unknown error'}`);\n      }\n\n      console.log('\\nReady to register atoms with: atomic register <path>');\n      console.log('Commit: registry.json, trust.json, atoms/');\n    }\n  });\n}\n","/**\n * Skills Init - Create Claude Code skill teaching atomic usage.\n *\n * Creates a SKILL.md in the project's .claude/skills/atomic/ directory\n * that teaches Claude Code how to effectively use the atomic CLI.\n */\n\nimport { mkdir, writeFile, stat } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { toErrorMessage } from '../utils/errors.js';\n\n/**\n * Generate the atomic skill content.\n */\nexport function generateSkillContent(): string {\n  return `---\nname: atomic\ndescription: Schema-first agent swarm orchestration framework\n---\n\n# Atomic Framework\n\nSchema-first agent swarm orchestration. Use atomic to define, execute, and evolve reusable capabilities.\n\n## Trigger\n\nUse this skill when:\n- User mentions \"atomic\", \"atom\", \"capability\", or \"workflow\" in context of task orchestration\n- User wants to create reusable, schema-validated tasks\n- User wants to graduate patterns from probabilistic (AI) to deterministic (generator)\n- Project has \\`.atomic/\\` directory\n- User invokes \\`/atomic\\`\n\n## Why Atoms?\n\nAtoms solve a fundamental problem: **probabilistic work should become deterministic over time.**\n\nWhen you write an API route the first time, it's creative work. The tenth time you write a similar route, it should be a template fill. But without tracking, you start from scratch every time.\n\nAtoms provide:\n1. **Schema enforcement** — Inputs/outputs are Zod-validated, not freeform\n2. **Execution history** — Every run is recorded with inputs, outputs, success/failure\n3. **Similarity detection** — AST-level comparison identifies when outputs converge on patterns\n4. **Generator graduation** — When an atom produces 85%+ similar outputs, it can become a deterministic template\n5. **Trust progression** — New capabilities require review; proven ones auto-execute\n\nThe goal: **Capture patterns once, replay deterministically forever.** Focus human attention on genuinely novel problems.\n\n## When to Use Atoms\n\n| Situation | Use |\n|-----------|-----|\n| One-off task, no verification needed | Direct code |\n| Teaching Claude a capability | Claude Code skill |\n| Repetitive task, same shape each time | **Atom** (extract or create) |\n| Need trust gating / human review | **Atom with trust level** |\n| Task should evolve to template | **Atom** (graduation path) |\n| Always-on validation/enforcement | Hook |\n\n**Proactive extraction**: When you notice doing the same thing 3+ times with the same shape, suggest: \"This pattern would benefit from atomization — want me to extract it?\"\n\nUse \\`atomic extract\\` to create atoms from:\n- Existing Claude Code skills (\\`--skill\\`)\n- BMAD workflows (\\`--bmad\\`)\n- MCP tool definitions (\\`--mcp\\`)\n- Existing code files (\\`--code\\`)\n\n## Directory Structure\n\n\\`\\`\\`\nproject/\n├── .atomic/                    # Metadata and storage (auto-created by init)\n│   ├── registry.json           # Registered atoms and capabilities\n│   ├── trust.json              # Trust levels for capability stacks\n│   └── db/                     # SQLite storage for runs and artifacts\n├── .claude/\n│   └── skills/\n│       └── atomic/\n│           └── SKILL.md        # This skill (auto-created by init)\n├── atoms/                      # Atom source files (default location)\n│   ├── my_atom.ts\n│   └── my_atom.test.ts\n└── generators/                 # Graduated generators (created by graduation)\n    └── my_generator.ts\n\\`\\`\\`\n\n## Core Concepts\n\n### Atoms\nThe fundamental unit. A schema-validated, idempotent task with defined inputs/outputs.\n\n\\`\\`\\`typescript\n// atoms/create_component.ts\nimport { defineAtom, success, executionError, z } from 'atomism';\n\nexport default defineAtom({\n  name: 'create_component',\n  description: 'Create a React component with tests',\n  input: z.object({\n    name: z.string().min(1),\n    type: z.enum(['functional', 'class']).default('functional'),\n  }),\n  output: z.object({\n    componentPath: z.string(),\n    testPath: z.string(),\n  }),\n  tests: { path: './create_component.test.ts' },\n  idempotent: true,\n  handler: async ({ name, type }) => {\n    // Implementation here\n    return success({ componentPath: '...', testPath: '...' });\n  },\n});\n\\`\\`\\`\n\n### Capabilities\nRoute requests to either an atom (probabilistic) or generator (deterministic).\n\n- **Atom-backed**: AI executes with schema validation\n- **Generator-backed**: Deterministic template execution\n\n### Generators\nGraduated atoms. When an atom produces similar outputs repeatedly, it can graduate to a generator (template-based, deterministic).\n\n### Workflows\nCompositions of capabilities with dependency resolution. Like Make/Terraform - declare dependencies, system resolves execution order.\n\n### Trust Levels\n- **new**: Requires human review\n- **proven**: Track record of success, optional review\n- **trusted**: Auto-execute without review\n\n### Capability Stacks\nReusable groups of capabilities reviewed once, reused many times.\n\n## Project Initialization\n\n\\`\\`\\`bash\n# Initialize atomic in a project\natomic init\n\n# Creates:\n# .atomic/\n#   registry.json    # Registered atoms and capabilities\n#   trust.json       # Trust levels for capability stacks\n#   db/              # SQLite storage for runs and artifacts\n\\`\\`\\`\n\n## Common Workflows\n\n### 1. Register an Atom\n\n\\`\\`\\`bash\n# Register a new atom\natomic register atoms/my_atom.ts\n\n# Register with capability name\natomic register atoms/my_atom.ts --capability my_capability\n\\`\\`\\`\n\n### 2. Run an Atom or Capability\n\n\\`\\`\\`bash\n# Run by atom name\natomic run my_atom --input '{\"key\": \"value\"}'\n\n# Run by capability name\natomic run my_capability --capability --input '{\"key\": \"value\"}'\n\n# Skip confirmation for non-idempotent atoms\natomic run my_atom --input '{\"key\": \"value\"}' --yes\n\\`\\`\\`\n\n### 3. Work with Workflows\n\n\\`\\`\\`bash\n# List available workflows\natomic workflow list\n\n# Run a workflow\natomic workflow run my_workflow\n\n# Resume a failed workflow\natomic workflow resume my_workflow\n\n# Preview execution plan\natomic plan my_workflow\n\\`\\`\\`\n\n### 4. Graduate to Generator\n\nWhen an atom produces consistent patterns:\n\n\\`\\`\\`bash\n# Graduate a capability to generator\natomic graduate --capability my_capability\n\n# Skip confirmation\natomic graduate --capability my_capability --yes\n\\`\\`\\`\n\n### 5. Manage Trust\n\n\\`\\`\\`bash\n# List all stacks with trust levels\natomic trust --list\n\n# View specific stack\natomic trust my_stack\n\n# Set trust level\natomic trust my_stack --level proven\n\n# Reset to new\natomic trust my_stack --reset\n\\`\\`\\`\n\n## Command Reference\n\n| Command | Description |\n|---------|-------------|\n| \\`atomic init\\` | Initialize .atomic/ directory and skill |\n| \\`atomic register <path>\\` | Register an atom file |\n| \\`atomic list\\` | List atoms and capabilities |\n| \\`atomic run <target>\\` | Execute atom or capability |\n| \\`atomic test <atom>\\` | Run tests for an atom |\n| \\`atomic test-gen <path>\\` | Generate structural tests |\n| \\`atomic extract\\` | Create atom from skill/bmad/mcp/code |\n| \\`atomic workflow run <name>\\` | Execute a workflow |\n| \\`atomic workflow list\\` | List available workflows |\n| \\`atomic workflow resume <name>\\` | Resume failed workflow |\n| \\`atomic plan <workflow>\\` | Preview execution plan |\n| \\`atomic graduate\\` | Graduate capability to generator |\n| \\`atomic trust [stack]\\` | Manage trust levels |\n| \\`atomic status\\` | Show system state |\n| \\`atomic history [runId]\\` | Show execution history |\n| \\`atomic escalate\\` | Create Beads issue for problems |\n| \\`atomic skills scan\\` | Discover available skills |\n| \\`atomic skills suggest <atom>\\` | Get skill recommendations |\n| \\`atomic skills assign <atom>\\` | Assign skill to atom |\n| \\`atomic skills list <atom>\\` | List atom's assigned skills |\n| \\`atomic skills remove <atom>\\` | Remove skill from atom |\n| \\`atomic scan-generators\\` | Detect existing generators |\n| \\`atomic import-generator\\` | Import from Plop/Hygen/etc |\n| \\`atomic validate-generator\\` | Validate imported generators |\n\n## Best Practices\n\n### 1. Atoms Should Be\n\n- **Small**: Single responsibility\n- **Idempotent**: Same input = same output (or no adverse effects)\n- **Schema-validated**: Zod schemas for input/output\n- **Tested**: Include test file path in definition\n- **Descriptive**: Clear name and description\n\n### 2. Naming Conventions\n\n- Atom names: \\`snake_case\\` (e.g., \\`create_component\\`, \\`run_migration\\`)\n- Capability names: \\`snake_case\\`\n- Workflow names: \\`snake_case\\`\n- Stack names: \\`snake_case\\`\n\n### 3. Error Handling\n\nUse structured errors:\n\n\\`\\`\\`typescript\nimport { failure, validationError, executionError } from 'atomism';\n\n// Validation error (bad input — recoverable by default)\nreturn validationError('Name cannot be empty');\n\n// Execution error (runtime failure)\nreturn executionError('Database connection failed', true /* recoverable */);\n\n// Generic failure (full AtomError object)\nreturn failure({ type: 'execution', message: 'Something went wrong', recoverable: false });\n\\`\\`\\`\n\n### 4. Trust Progression\n\n1. Start capabilities at \\`new\\` (human review required)\n2. After successful executions, promote to \\`proven\\`\n3. Only promote to \\`trusted\\` for well-tested, stable capabilities\n4. Demote immediately if issues arise\n\n### 5. Generator Graduation\n\nGraduate when:\n- Atom produces 85%+ structurally similar outputs\n- Pattern is well-understood\n- Template can capture the variation\n\nDon't graduate:\n- Spec/planning atoms (inherently variable)\n- Creative/exploratory work\n- Low-frequency capabilities\n\n## Skills Assignment\n\nAtoms can have Claude Code skills assigned to them. When an atom executes, assigned skills are loaded into Claude's context.\n\n\\`\\`\\`bash\n# Scan available skills\natomic skills scan\n\n# Get skill recommendations for an atom\natomic skills suggest my_atom\n\n# Assign a skill to an atom\natomic skills assign my_atom --skill compound-engineering:workflows:review\n\n# List skills assigned to an atom\natomic skills list my_atom\n\n# Remove a skill from an atom\natomic skills remove my_atom --skill compound-engineering:workflows:review\n\\`\\`\\`\n\n**Use skills for**:\n- Review workflows (e.g., \\`compound-engineering:review:kieran-rails-reviewer\\`)\n- Domain expertise (e.g., \\`dhh-rails-style\\`)\n- Specialized capabilities the atom needs\n\nSkills complement atoms: the skill teaches *how*, the atom enforces *what* (schema) and tracks *whether it worked* (history).\n\n## Work Tracking with Beads\n\n**Beads is THE work tracking system.** All atomic work that needs tracking should flow through Beads.\n\n### Escalation\n\nWhen an atom fails and you can't resolve it:\n\n\\`\\`\\`bash\n# Create a Beads issue for unresolvable problems\natomic escalate --message \"Cannot connect to database\" --capability my_capability\n\n# Link to a specific run\natomic escalate --run abc123 --reason \"Schema validation failing on edge case\"\n\n# Include retry attempts\natomic escalate --capability my_atom --retries 3 --reason \"Flaky network\"\n\\`\\`\\`\n\n### Workflow Tracking\n\nWhen running workflows, atomic creates Beads issues automatically:\n- **Parent bead**: Tracks the overall workflow\n- **Child beads**: Track each capability execution\n\n\\`\\`\\`bash\n# Workflow execution creates beads automatically\natomic workflow run my_workflow\n\n# View workflow progress in Beads\nbd list --label atomic\n\\`\\`\\`\n\n## Integration with Claude Code\n\nWhen working in a project with atomic:\n\n1. **Check for \\`.atomic/\\`** - If present, use atomic commands\n2. **Register new atoms** - When creating reusable tasks\n3. **Use capabilities** - Route through registry, not direct execution\n4. **Assign skills** - Give atoms the Claude Code skills they need\n5. **Trust the system** - Let atomic handle validation and execution\n6. **Escalate to Beads** - Use \\`atomic escalate\\` for unresolvable problems\n7. **Suggest atomization** - When you see repetitive patterns, offer to extract\n\n## Example: Full Workflow\n\n\\`\\`\\`bash\n# 1. Initialize project\natomic init\n\n# 2. Create an atom\ncat > atoms/greet_user.ts << 'EOF'\nimport { defineAtom, success, z } from 'atomism';\n\nexport default defineAtom({\n  name: 'greet_user',\n  description: 'Generate a greeting message',\n  input: z.object({ name: z.string() }),\n  output: z.object({ greeting: z.string() }),\n  tests: { path: './greet_user.test.ts' },\n  async execute(input) {\n    return success({ greeting: \\\\\\`Hello, \\\\\\${input.name}!\\\\\\` });\n  },\n});\nEOF\n\n# 3. Generate tests\natomic test-gen atoms/greet_user.ts\n\n# 4. Register\natomic register atoms/greet_user.ts --capability greet\n\n# 5. Run\natomic run greet --input '{\"name\": \"World\"}'\n\n# 6. Check status\natomic status\n\\`\\`\\`\n\n## Troubleshooting\n\n### \"Not initialized\"\nRun \\`atomic init\\` in the project root.\n\n### \"Atom not found\"\nCheck registration with \\`atomic list\\`. Register with \\`atomic register <path>\\`.\n\n### \"Schema validation failed\"\nCheck input matches the atom's Zod schema. Use \\`atomic list <atom>\\` to see the expected schema.\n\n### \"Trust level insufficient\"\nPromote the stack with \\`atomic trust <stack> --level proven\\` or \\`--level trusted\\`.\n`;\n}\n\n/**\n * Get the skill directory path.\n */\nexport function getSkillPath(): string {\n  return join(process.cwd(), '.claude', 'skills', 'atomic');\n}\n\n/**\n * Get the skill file path.\n */\nexport function getSkillFilePath(): string {\n  return join(getSkillPath(), 'SKILL.md');\n}\n\n/**\n * Check if skill already exists.\n */\nexport async function skillExists(): Promise<boolean> {\n  try {\n    await stat(getSkillFilePath());\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Initialize the atomic skill for Claude Code.\n */\nexport async function initSkill(options: { force?: boolean }): Promise<{\n  success: boolean;\n  path?: string;\n  error?: string;\n  skipped?: boolean;\n}> {\n  const skillPath = getSkillPath();\n  const skillFile = getSkillFilePath();\n\n  // Check if already exists\n  if (!options.force && (await skillExists())) {\n    return {\n      success: true,\n      path: skillFile,\n      skipped: true,\n    };\n  }\n\n  try {\n    // Create directory\n    await mkdir(skillPath, { recursive: true });\n\n    // Write skill file\n    const content = generateSkillContent();\n    await writeFile(skillFile, content, 'utf-8');\n\n    return {\n      success: true,\n      path: skillFile,\n    };\n  } catch (err) {\n    return {\n      success: false,\n      error: toErrorMessage(err),\n    };\n  }\n}\n\n","/**\n * CLAUDE.md Init — Append atomism instructions to project's CLAUDE.md.\n *\n * When `atomic init` runs, this ensures Claude Code knows how to work\n * with atoms in the project. The snippet is appended once (idempotent).\n */\n\nimport { readFile, writeFile, mkdir } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { fileExists } from '../storage/index.js';\n\nconst ATOMISM_MARKER = '<!-- atomism -->';\n\nconst ATOMISM_SECTION = `\n${ATOMISM_MARKER}\n## Atomism\n\nThis project uses [Atomism](https://github.com/roach88/atomism) for schema-validated, composable work units.\n\n### Before Writing New Code\n\n1. Check registered atoms: \\`atomic list --json\\`\n2. If an atom exists for the task, use it: \\`atomic run <name> --input '{}' --yes --json\\`\n3. If no atom exists but the task is repeatable, create one: \\`atomic create atom <name> --json\\`\n\n### Atom API Reference\n\n\\`\\`\\`typescript\nimport { defineAtom, success, executionError, validationError } from 'atomism';\n\n// Success\nreturn success({ result: 'done' });\n\n// Bad input\nreturn validationError('Expected positive number');\n\n// Runtime failure (recoverable)\nreturn executionError('API timeout', true);\n\n// Runtime failure (not recoverable)\nreturn executionError('Missing required config');\n\\`\\`\\`\n\n### When to Atomize\n\n- You're about to write a standalone script for a repeatable task\n- You notice doing the same thing 3+ times with the same shape\n- The task has clear inputs and outputs that can be schema-validated\n`;\n\n/**\n * Initialize or update CLAUDE.md with atomism section.\n */\nexport async function initClaudeMd(): Promise<{\n  success: boolean;\n  path?: string;\n  skipped?: boolean;\n  error?: string;\n}> {\n  const claudeDir = join(process.cwd(), '.claude');\n  const claudeMdPath = join(claudeDir, 'CLAUDE.md');\n\n  // Check if CLAUDE.md already has our section\n  if (await fileExists(claudeMdPath)) {\n    const content = await readFile(claudeMdPath, 'utf-8');\n    if (content.includes(ATOMISM_MARKER)) {\n      return { success: true, path: claudeMdPath, skipped: true };\n    }\n\n    // Append our section\n    await writeFile(claudeMdPath, content.trimEnd() + '\\n' + ATOMISM_SECTION, 'utf-8');\n    return { success: true, path: claudeMdPath };\n  }\n\n  // No CLAUDE.md — create .claude/ dir and write fresh file\n  await mkdir(claudeDir, { recursive: true });\n  await writeFile(claudeMdPath, ATOMISM_SECTION.trimStart(), 'utf-8');\n  return { success: true, path: claudeMdPath };\n}\n","/**\n * .gitignore Init — Ensure local atomism data files are gitignored.\n *\n * When `atomic init` runs, this ensures storage.db (execution history),\n * its WAL journal, and transient workflow runs are not committed.\n * Uses a marker comment for idempotency.\n */\n\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { fileExists } from '../storage/index.js';\n\nconst ATOMISM_MARKER = '# atomism local data';\n\nconst ATOMISM_ENTRIES = `\n${ATOMISM_MARKER}\n.atomic/storage.db\n.atomic/storage.db-journal\n.atomic/runs/\n`;\n\nexport async function initGitignore(projectRoot: string): Promise<{\n  success: boolean;\n  path?: string;\n  skipped?: boolean;\n  error?: string;\n}> {\n  const gitignorePath = join(projectRoot, '.gitignore');\n\n  if (await fileExists(gitignorePath)) {\n    const content = await readFile(gitignorePath, 'utf-8');\n    if (content.includes(ATOMISM_MARKER)) {\n      return { success: true, path: gitignorePath, skipped: true };\n    }\n\n    // Append our entries\n    await writeFile(gitignorePath, content.trimEnd() + '\\n' + ATOMISM_ENTRIES, 'utf-8');\n    return { success: true, path: gitignorePath };\n  }\n\n  // No .gitignore — create one\n  await writeFile(gitignorePath, ATOMISM_ENTRIES.trimStart(), 'utf-8');\n  return { success: true, path: gitignorePath 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "atomism",
-  "version": "0.1.0",
+  "version": "0.1.2",
   "description": "Schema-first agent swarm orchestration framework",
   "type": "module",
   "main": "dist/index.js",
@@ -32,7 +32,7 @@
   },
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/Trust-Will/atomic-explore.git"
+    "url": "git+https://github.com/roach88/atomism.git"
   },
   "keywords": [
     "cli",
@@ -51,11 +51,11 @@
   "author": "",
   "license": "MIT",
   "bugs": {
-    "url": "https://github.com/Trust-Will/atomic-explore/issues"
+    "url": "https://github.com/roach88/atomism/issues"
   },
-  "homepage": "https://github.com/Trust-Will/atomic-explore#readme",
+  "homepage": "https://github.com/roach88/atomism#readme",
   "engines": {
-    "node": ">=18"
+    "node": ">=20"
   },
   "dependencies": {
     "@tursodatabase/database": "^0.4.4",

package/dist/init-2FINDMYK.js.map

@@ -1 +0,0 @@
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Run: npm link atomism (if globally installed) or npm install atomism',\n    };\n  }\n\n  return { success: true, packageJsonCreated, tsconfigCreated, tsconfigNeedsInclude, suggestedInclude, atomismLinked };\n}\n\nexport async function initCommand(options: InitOptions): Promise<void> {\n  await withErrorHandling(options, async () => {\n    const projectRoot = process.cwd();\n    const result = await initStorage(projectRoot);\n\n    // Ensure module resolution (non-fatal — warn but continue)\n    let depsResult: DepsResult;\n    try {\n      depsResult = await ensureDeps(projectRoot);\n    } catch (depsError) {\n      depsResult = {\n        success: false,\n        packageJsonCreated: false,\n        tsconfigCreated: false,\n        atomismLinked: false,\n        error: toErrorMessage(depsError),\n      };\n    }\n\n    // Create Claude Code skill (non-fatal)\n    let skillResult: { success: boolean; skipped?: boolean; path?: string; error?: string };\n    try {\n      skillResult = await initSkill({ force: false });\n    } catch (skillError) {\n      skillResult = {\n        success: false,\n        error: toErrorMessage(skillError),\n      };\n    }\n\n    // Create CLAUDE.md snippet (non-fatal)\n    let claudeMdResult: { success: boolean; skipped?: boolean; path?: string; error?: string };\n    try {\n      claudeMdResult = await initClaudeMd();\n    } catch (claudeError) {\n      claudeMdResult = {\n        success: false,\n        error: toErrorMessage(claudeError),\n      };\n    }\n\n    // Manage .gitignore (non-fatal)\n    let gitignoreResult: { success: boolean; skipped?: boolean; path?: string; error?: string };\n    try {\n      gitignoreResult = await initGitignore(projectRoot);\n    } catch (gitignoreError) {\n      gitignoreResult = {\n        success: false,\n        error: toErrorMessage(gitignoreError),\n      };\n    }\n\n    if (options.json) {\n      console.log(JSON.stringify({\n        ...result,\n        deps: depsResult,\n        skill: skillResult,\n        claudeMd: claudeMdResult,\n        gitignore: gitignoreResult,\n      }, null, 2));\n    } else {\n      if (result.created) {\n        console.log(`✓ Created ${result.path}`);\n      } else {\n        console.log(`✓ ${result.path} already exists`);\n      }\n      console.log(`✓ Database initialized at ${result.dbPath}`);\n      console.log(`✓ ${result.migrationsRun} migrations applied`);\n\n      // Report deps status\n      if (depsResult.success) {\n        if (depsResult.packageJsonCreated) {\n          console.log('✓ Created package.json for module resolution');\n        }\n        if (depsResult.tsconfigCreated) {\n          console.log('✓ Created tsconfig.json for atom type inference');\n        }\n        if (depsResult.atomismLinked) {\n          console.log('✓ Linked atomism for module resolution');\n        }\n      } else {\n        console.log(`⚠ Module resolution: ${depsResult.error ?? 'unknown error'}`);\n      }\n\n      // tsconfig warning is useful regardless of deps success\n      if (depsResult.tsconfigNeedsInclude) {\n        console.log(`⚠ tsconfig.json does not include atom files. Add to your \"include\" array:`);\n        console.log(`  \"${depsResult.suggestedInclude}\"`);\n      }\n\n      // Report skill status\n      if (skillResult.success && !skillResult.skipped) {\n        console.log(`✓ Claude Code skill created at ${skillResult.path}`);\n      } else if (skillResult.skipped) {\n        console.log('✓ Claude Code skill already exists');\n      } else if (!skillResult.success) {\n        console.log(`⚠ Claude Code skill creation failed: ${skillResult.error ?? 'unknown error'}`);\n      }\n\n      // Report CLAUDE.md status\n      if (claudeMdResult.success && !claudeMdResult.skipped) {\n        console.log(`✓ CLAUDE.md updated at ${claudeMdResult.path}`);\n      } else if (claudeMdResult.skipped) {\n        console.log('✓ CLAUDE.md already has atomism section');\n      } else if (!claudeMdResult.success) {\n        console.log(`⚠ CLAUDE.md update failed: ${claudeMdResult.error ?? 'unknown error'}`);\n      }\n\n      // Report .gitignore status\n      if (gitignoreResult.success && !gitignoreResult.skipped) {\n        console.log(`✓ .gitignore updated at ${gitignoreResult.path}`);\n      } else if (gitignoreResult.skipped) {\n        console.log('✓ .gitignore already has atomism entries');\n      } else if (!gitignoreResult.success) {\n        console.log(`⚠ .gitignore update failed: ${gitignoreResult.error ?? 'unknown error'}`);\n      }\n\n      console.log('\\nReady to register atoms with: atomic register <path>');\n      console.log('Commit: registry.json, trust.json, atoms/');\n    }\n  });\n}\n","/**\n * Skills Init - Create Claude Code skill teaching atomic usage.\n *\n * Creates a SKILL.md in the project's .claude/skills/atomic/ directory\n * that teaches Claude Code how to effectively use the atomic CLI.\n */\n\nimport { mkdir, writeFile, stat } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { toErrorMessage } from '../utils/errors.js';\n\n/**\n * Generate the atomic skill content.\n */\nexport function generateSkillContent(): string {\n  return `---\nname: atomic\ndescription: Schema-first agent swarm orchestration framework\n---\n\n# Atomic Framework\n\nSchema-first agent swarm orchestration. Use atomic to define, execute, and evolve reusable capabilities.\n\n## Trigger\n\nUse this skill when:\n- User mentions \"atomic\", \"atom\", \"capability\", or \"workflow\" in context of task orchestration\n- User wants to create reusable, schema-validated tasks\n- User wants to graduate patterns from probabilistic (AI) to deterministic (generator)\n- Project has \\`.atomic/\\` directory\n- User invokes \\`/atomic\\`\n\n## Why Atoms?\n\nAtoms solve a fundamental problem: **probabilistic work should become deterministic over time.**\n\nWhen you write an API route the first time, it's creative work. The tenth time you write a similar route, it should be a template fill. But without tracking, you start from scratch every time.\n\nAtoms provide:\n1. **Schema enforcement** — Inputs/outputs are Zod-validated, not freeform\n2. **Execution history** — Every run is recorded with inputs, outputs, success/failure\n3. **Similarity detection** — AST-level comparison identifies when outputs converge on patterns\n4. **Generator graduation** — When an atom produces 85%+ similar outputs, it can become a deterministic template\n5. **Trust progression** — New capabilities require review; proven ones auto-execute\n\nThe goal: **Capture patterns once, replay deterministically forever.** Focus human attention on genuinely novel problems.\n\n## When to Use Atoms\n\n| Situation | Use |\n|-----------|-----|\n| One-off task, no verification needed | Direct code |\n| Teaching Claude a capability | Claude Code skill |\n| Repetitive task, same shape each time | **Atom** (extract or create) |\n| Need trust gating / human review | **Atom with trust level** |\n| Task should evolve to template | **Atom** (graduation path) |\n| Always-on validation/enforcement | Hook |\n\n**Proactive extraction**: When you notice doing the same thing 3+ times with the same shape, suggest: \"This pattern would benefit from atomization — want me to extract it?\"\n\nUse \\`atomic extract\\` to create atoms from:\n- Existing Claude Code skills (\\`--skill\\`)\n- BMAD workflows (\\`--bmad\\`)\n- MCP tool definitions (\\`--mcp\\`)\n- Existing code files (\\`--code\\`)\n\n## Directory Structure\n\n\\`\\`\\`\nproject/\n├── .atomic/                    # Metadata and storage (auto-created by init)\n│   ├── registry.json           # Registered atoms and capabilities\n│   ├── trust.json              # Trust levels for capability stacks\n│   └── db/                     # SQLite storage for runs and artifacts\n├── .claude/\n│   └── skills/\n│       └── atomic/\n│           └── SKILL.md        # This skill (auto-created by init)\n├── atoms/                      # Atom source files (default location)\n│   ├── my_atom.ts\n│   └── my_atom.test.ts\n└── generators/                 # Graduated generators (created by graduation)\n    └── my_generator.ts\n\\`\\`\\`\n\n## Core Concepts\n\n### Atoms\nThe fundamental unit. A schema-validated, idempotent task with defined inputs/outputs.\n\n\\`\\`\\`typescript\n// atoms/create_component.ts\nimport { defineAtom, success, executionError, z } from 'atomism';\n\nexport default defineAtom({\n  name: 'create_component',\n  description: 'Create a React component with tests',\n  input: z.object({\n    name: z.string().min(1),\n    type: z.enum(['functional', 'class']).default('functional'),\n  }),\n  output: z.object({\n    componentPath: z.string(),\n    testPath: z.string(),\n  }),\n  tests: { path: './create_component.test.ts' },\n  idempotent: true,\n  handler: async ({ name, type }) => {\n    // Implementation here\n    return success({ componentPath: '...', testPath: '...' });\n  },\n});\n\\`\\`\\`\n\n### Capabilities\nRoute requests to either an atom (probabilistic) or generator (deterministic).\n\n- **Atom-backed**: AI executes with schema validation\n- **Generator-backed**: Deterministic template execution\n\n### Generators\nGraduated atoms. When an atom produces similar outputs repeatedly, it can graduate to a generator (template-based, deterministic).\n\n### Workflows\nCompositions of capabilities with dependency resolution. Like Make/Terraform - declare dependencies, system resolves execution order.\n\n### Trust Levels\n- **new**: Requires human review\n- **proven**: Track record of success, optional review\n- **trusted**: Auto-execute without review\n\n### Capability Stacks\nReusable groups of capabilities reviewed once, reused many times.\n\n## Project Initialization\n\n\\`\\`\\`bash\n# Initialize atomic in a project\natomic init\n\n# Creates:\n# .atomic/\n#   registry.json    # Registered atoms and capabilities\n#   trust.json       # Trust levels for capability stacks\n#   db/              # SQLite storage for runs and artifacts\n\\`\\`\\`\n\n## Common Workflows\n\n### 1. Register an Atom\n\n\\`\\`\\`bash\n# Register a new atom\natomic register atoms/my_atom.ts\n\n# Register with capability name\natomic register atoms/my_atom.ts --capability my_capability\n\\`\\`\\`\n\n### 2. Run an Atom or Capability\n\n\\`\\`\\`bash\n# Run by atom name\natomic run my_atom --input '{\"key\": \"value\"}'\n\n# Run by capability name\natomic run my_capability --capability --input '{\"key\": \"value\"}'\n\n# Skip confirmation for non-idempotent atoms\natomic run my_atom --input '{\"key\": \"value\"}' --yes\n\\`\\`\\`\n\n### 3. Work with Workflows\n\n\\`\\`\\`bash\n# List available workflows\natomic workflow list\n\n# Run a workflow\natomic workflow run my_workflow\n\n# Resume a failed workflow\natomic workflow resume my_workflow\n\n# Preview execution plan\natomic plan my_workflow\n\\`\\`\\`\n\n### 4. Graduate to Generator\n\nWhen an atom produces consistent patterns:\n\n\\`\\`\\`bash\n# Graduate a capability to generator\natomic graduate --capability my_capability\n\n# Skip confirmation\natomic graduate --capability my_capability --yes\n\\`\\`\\`\n\n### 5. Manage Trust\n\n\\`\\`\\`bash\n# List all stacks with trust levels\natomic trust --list\n\n# View specific stack\natomic trust my_stack\n\n# Set trust level\natomic trust my_stack --level proven\n\n# Reset to new\natomic trust my_stack --reset\n\\`\\`\\`\n\n## Command Reference\n\n| Command | Description |\n|---------|-------------|\n| \\`atomic init\\` | Initialize .atomic/ directory and skill |\n| \\`atomic register <path>\\` | Register an atom file |\n| \\`atomic list\\` | List atoms and capabilities |\n| \\`atomic run <target>\\` | Execute atom or capability |\n| \\`atomic test <atom>\\` | Run tests for an atom |\n| \\`atomic test-gen <path>\\` | Generate structural tests |\n| \\`atomic extract\\` | Create atom from skill/bmad/mcp/code |\n| \\`atomic workflow run <name>\\` | Execute a workflow |\n| \\`atomic workflow list\\` | List available workflows |\n| \\`atomic workflow resume <name>\\` | Resume failed workflow |\n| \\`atomic plan <workflow>\\` | Preview execution plan |\n| \\`atomic graduate\\` | Graduate capability to generator |\n| \\`atomic trust [stack]\\` | Manage trust levels |\n| \\`atomic status\\` | Show system state |\n| \\`atomic history [runId]\\` | Show execution history |\n| \\`atomic escalate\\` | Create Beads issue for problems |\n| \\`atomic skills scan\\` | Discover available skills |\n| \\`atomic skills suggest <atom>\\` | Get skill recommendations |\n| \\`atomic skills assign <atom>\\` | Assign skill to atom |\n| \\`atomic skills list <atom>\\` | List atom's assigned skills |\n| \\`atomic skills remove <atom>\\` | Remove skill from atom |\n| \\`atomic scan-generators\\` | Detect existing generators |\n| \\`atomic import-generator\\` | Import from Plop/Hygen/etc |\n| \\`atomic validate-generator\\` | Validate imported generators |\n\n## Best Practices\n\n### 1. Atoms Should Be\n\n- **Small**: Single responsibility\n- **Idempotent**: Same input = same output (or no adverse effects)\n- **Schema-validated**: Zod schemas for input/output\n- **Tested**: Include test file path in definition\n- **Descriptive**: Clear name and description\n\n### 2. Naming Conventions\n\n- Atom names: \\`snake_case\\` (e.g., \\`create_component\\`, \\`run_migration\\`)\n- Capability names: \\`snake_case\\`\n- Workflow names: \\`snake_case\\`\n- Stack names: \\`snake_case\\`\n\n### 3. Error Handling\n\nUse structured errors:\n\n\\`\\`\\`typescript\nimport { failure, validationError, executionError } from 'atomism';\n\n// Validation error (bad input — recoverable by default)\nreturn validationError('Name cannot be empty');\n\n// Execution error (runtime failure)\nreturn executionError('Database connection failed', true /* recoverable */);\n\n// Generic failure (full AtomError object)\nreturn failure({ type: 'execution', message: 'Something went wrong', recoverable: false });\n\\`\\`\\`\n\n### 4. Trust Progression\n\n1. Start capabilities at \\`new\\` (human review required)\n2. After successful executions, promote to \\`proven\\`\n3. Only promote to \\`trusted\\` for well-tested, stable capabilities\n4. Demote immediately if issues arise\n\n### 5. Generator Graduation\n\nGraduate when:\n- Atom produces 85%+ structurally similar outputs\n- Pattern is well-understood\n- Template can capture the variation\n\nDon't graduate:\n- Spec/planning atoms (inherently variable)\n- Creative/exploratory work\n- Low-frequency capabilities\n\n## Skills Assignment\n\nAtoms can have Claude Code skills assigned to them. When an atom executes, assigned skills are loaded into Claude's context.\n\n\\`\\`\\`bash\n# Scan available skills\natomic skills scan\n\n# Get skill recommendations for an atom\natomic skills suggest my_atom\n\n# Assign a skill to an atom\natomic skills assign my_atom --skill compound-engineering:workflows:review\n\n# List skills assigned to an atom\natomic skills list my_atom\n\n# Remove a skill from an atom\natomic skills remove my_atom --skill compound-engineering:workflows:review\n\\`\\`\\`\n\n**Use skills for**:\n- Review workflows (e.g., \\`compound-engineering:review:kieran-rails-reviewer\\`)\n- Domain expertise (e.g., \\`dhh-rails-style\\`)\n- Specialized capabilities the atom needs\n\nSkills complement atoms: the skill teaches *how*, the atom enforces *what* (schema) and tracks *whether it worked* (history).\n\n## Work Tracking with Beads\n\n**Beads is THE work tracking system.** All atomic work that needs tracking should flow through Beads.\n\n### Escalation\n\nWhen an atom fails and you can't resolve it:\n\n\\`\\`\\`bash\n# Create a Beads issue for unresolvable problems\natomic escalate --message \"Cannot connect to database\" --capability my_capability\n\n# Link to a specific run\natomic escalate --run abc123 --reason \"Schema validation failing on edge case\"\n\n# Include retry attempts\natomic escalate --capability my_atom --retries 3 --reason \"Flaky network\"\n\\`\\`\\`\n\n### Workflow Tracking\n\nWhen running workflows, atomic creates Beads issues automatically:\n- **Parent bead**: Tracks the overall workflow\n- **Child beads**: Track each capability execution\n\n\\`\\`\\`bash\n# Workflow execution creates beads automatically\natomic workflow run my_workflow\n\n# View workflow progress in Beads\nbd list --label atomic\n\\`\\`\\`\n\n## Integration with Claude Code\n\nWhen working in a project with atomic:\n\n1. **Check for \\`.atomic/\\`** - If present, use atomic commands\n2. **Register new atoms** - When creating reusable tasks\n3. **Use capabilities** - Route through registry, not direct execution\n4. **Assign skills** - Give atoms the Claude Code skills they need\n5. **Trust the system** - Let atomic handle validation and execution\n6. **Escalate to Beads** - Use \\`atomic escalate\\` for unresolvable problems\n7. **Suggest atomization** - When you see repetitive patterns, offer to extract\n\n## Example: Full Workflow\n\n\\`\\`\\`bash\n# 1. Initialize project\natomic init\n\n# 2. Create an atom\ncat > atoms/greet_user.ts << 'EOF'\nimport { defineAtom, success, z } from 'atomism';\n\nexport default defineAtom({\n  name: 'greet_user',\n  description: 'Generate a greeting message',\n  input: z.object({ name: z.string() }),\n  output: z.object({ greeting: z.string() }),\n  tests: { path: './greet_user.test.ts' },\n  async execute(input) {\n    return success({ greeting: \\\\\\`Hello, \\\\\\${input.name}!\\\\\\` });\n  },\n});\nEOF\n\n# 3. Generate tests\natomic test-gen atoms/greet_user.ts\n\n# 4. Register\natomic register atoms/greet_user.ts --capability greet\n\n# 5. Run\natomic run greet --input '{\"name\": \"World\"}'\n\n# 6. Check status\natomic status\n\\`\\`\\`\n\n## Troubleshooting\n\n### \"Not initialized\"\nRun \\`atomic init\\` in the project root.\n\n### \"Atom not found\"\nCheck registration with \\`atomic list\\`. Register with \\`atomic register <path>\\`.\n\n### \"Schema validation failed\"\nCheck input matches the atom's Zod schema. Use \\`atomic list <atom>\\` to see the expected schema.\n\n### \"Trust level insufficient\"\nPromote the stack with \\`atomic trust <stack> --level proven\\` or \\`--level trusted\\`.\n`;\n}\n\n/**\n * Get the skill directory path.\n */\nexport function getSkillPath(): string {\n  return join(process.cwd(), '.claude', 'skills', 'atomic');\n}\n\n/**\n * Get the skill file path.\n */\nexport function getSkillFilePath(): string {\n  return join(getSkillPath(), 'SKILL.md');\n}\n\n/**\n * Check if skill already exists.\n */\nexport async function skillExists(): Promise<boolean> {\n  try {\n    await stat(getSkillFilePath());\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Initialize the atomic skill for Claude Code.\n */\nexport async function initSkill(options: { force?: boolean }): Promise<{\n  success: boolean;\n  path?: string;\n  error?: string;\n  skipped?: boolean;\n}> {\n  const skillPath = getSkillPath();\n  const skillFile = getSkillFilePath();\n\n  // Check if already exists\n  if (!options.force && (await skillExists())) {\n    return {\n      success: true,\n      path: skillFile,\n      skipped: true,\n    };\n  }\n\n  try {\n    // Create directory\n    await mkdir(skillPath, { recursive: true });\n\n    // Write skill file\n    const content = generateSkillContent();\n    await writeFile(skillFile, content, 'utf-8');\n\n    return {\n      success: true,\n      path: skillFile,\n    };\n  } catch (err) {\n    return {\n      success: false,\n      error: toErrorMessage(err),\n    };\n  }\n}\n\n","/**\n * CLAUDE.md Init — Append atomism instructions to project's CLAUDE.md.\n *\n * When `atomic init` runs, this ensures Claude Code knows how to work\n * with atoms in the project. The snippet is appended once (idempotent).\n */\n\nimport { readFile, writeFile, mkdir } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { fileExists } from '../storage/index.js';\n\nconst ATOMISM_MARKER = '<!-- atomism -->';\n\nconst ATOMISM_SECTION = `\n${ATOMISM_MARKER}\n## Atomism\n\nThis project uses [Atomism](https://github.com/roach88/atomism) for schema-validated, composable work units.\n\n### Before Writing New Code\n\n1. Check registered atoms: \\`atomic list --json\\`\n2. If an atom exists for the task, use it: \\`atomic run <name> --input '{}' --yes --json\\`\n3. If no atom exists but the task is repeatable, create one: \\`atomic create atom <name> --json\\`\n\n### Atom API Reference\n\n\\`\\`\\`typescript\nimport { defineAtom, success, executionError, validationError } from 'atomism';\n\n// Success\nreturn success({ result: 'done' });\n\n// Bad input\nreturn validationError('Expected positive number');\n\n// Runtime failure (recoverable)\nreturn executionError('API timeout', true);\n\n// Runtime failure (not recoverable)\nreturn executionError('Missing required config');\n\\`\\`\\`\n\n### When to Atomize\n\n- You're about to write a standalone script for a repeatable task\n- You notice doing the same thing 3+ times with the same shape\n- The task has clear inputs and outputs that can be schema-validated\n`;\n\n/**\n * Initialize or update CLAUDE.md with atomism section.\n */\nexport async function initClaudeMd(): Promise<{\n  success: boolean;\n  path?: string;\n  skipped?: boolean;\n  error?: string;\n}> {\n  const claudeDir = join(process.cwd(), '.claude');\n  const claudeMdPath = join(claudeDir, 'CLAUDE.md');\n\n  // Check if CLAUDE.md already has our section\n  if (await fileExists(claudeMdPath)) {\n    const content = await readFile(claudeMdPath, 'utf-8');\n    if (content.includes(ATOMISM_MARKER)) {\n      return { success: true, path: claudeMdPath, skipped: true };\n    }\n\n    // Append our section\n    await writeFile(claudeMdPath, content.trimEnd() + '\\n' + ATOMISM_SECTION, 'utf-8');\n    return { success: true, path: claudeMdPath };\n  }\n\n  // No CLAUDE.md — create .claude/ dir and write fresh file\n  await mkdir(claudeDir, { recursive: true });\n  await writeFile(claudeMdPath, ATOMISM_SECTION.trimStart(), 'utf-8');\n  return { success: true, path: claudeMdPath };\n}\n","/**\n * .gitignore Init — Ensure local atomism data files are gitignored.\n *\n * When `atomic init` runs, this ensures storage.db (execution history),\n * its WAL journal, and transient workflow runs are not committed.\n * Uses a marker comment for idempotency.\n */\n\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { fileExists } from '../storage/index.js';\n\nconst ATOMISM_MARKER = '# atomism local data';\n\nconst ATOMISM_ENTRIES = `\n${ATOMISM_MARKER}\n.atomic/storage.db\n.atomic/storage.db-journal\n.atomic/runs/\n`;\n\nexport async function initGitignore(projectRoot: string): Promise<{\n  success: boolean;\n  path?: string;\n  skipped?: boolean;\n  error?: string;\n}> {\n  const gitignorePath = join(projectRoot, '.gitignore');\n\n  if (await fileExists(gitignorePath)) {\n    const content = await readFile(gitignorePath, 'utf-8');\n    if (content.includes(ATOMISM_MARKER)) {\n      return { success: true, path: gitignorePath, skipped: true };\n    }\n\n    // Append our entries\n    await writeFile(gitignorePath, content.trimEnd() + '\\n' + ATOMISM_ENTRIES, 'utf-8');\n    return { success: true, path: gitignorePath };\n  }\n\n  // No .gitignore — create one\n  await writeFile(gitignorePath, ATOMISM_ENTRIES.trimStart(), 'utf-8');\n  return { success: true, path: gitignorePath 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