musubix2 0.5.5 → 0.5.7

package/.claude/.musubix-managed

@@ -1 +1 @@
-{"generator":"musubix2","version":"0.5.5","timestamp":"2026-07-09T09:31:00.078Z"}
+{"generator":"musubix2","version":"0.5.7","timestamp":"2026-07-09T10:10:51.798Z"}

package/dist/assets/skills-manifest.json

@@ -1,6 +1,6 @@
 {
   "version": "1.0",
-  "generatedAt": "2026-07-09T09:31:00.109Z",
+  "generatedAt": "2026-07-09T10:10:51.826Z",
   "entries": [
     {
       "platform": "copilot",

package/dist/cli.d.ts

@@ -67,10 +67,26 @@ export declare function handleTasksValidate(filePath: string): Promise<ExitCodeV
 export declare function handleTasksList(filePath?: string): Promise<ExitCodeValue>;
 export declare function handleTasksStats(filePath?: string): Promise<ExitCodeValue>;
 export declare function handleInit(targetPath?: string, name?: string, force?: boolean): Promise<ExitCodeValue>;
-export declare function handleTrace(sub: string | undefined, args: string[]): Promise<ExitCodeValue>;
-export declare function handleTraceVerify(): Promise<ExitCodeValue>;
+interface CodeTraceData {
+    requirementIds: string[];
+    fileIds: string[];
+    links: Array<{
+        source: string;
+        target: string;
+        verified: boolean;
+    }>;
+    refsByReq: Map<string, string[]>;
+}
+/**
+ * Build real traceability data by parsing requirement ids from the specs file
+ * and scanning source files for `REQ-XXX-NNN` references. A requirement is
+ * "covered" when at least one source file references it.
+ */
+export declare function buildCodeTraceData(specsFile: string, srcDir: string): CodeTraceData;
+export declare function handleTrace(sub: string | undefined, args: string[], flags?: Record<string, unknown>): Promise<ExitCodeValue>;
+export declare function handleTraceVerify(flags?: Record<string, unknown>): Promise<ExitCodeValue>;
 export declare function handlePolicy(sub: string | undefined, args: string[]): Promise<ExitCodeValue>;
-export declare function handleOntology(sub: string | undefined): Promise<ExitCodeValue>;
+export declare function handleOntology(sub: string | undefined, args?: string[]): Promise<ExitCodeValue>;
 /**
  * Collect files from a path. A file returns itself; a directory is walked
  * recursively (skipping common vendor/build dirs). Optionally filter by
@@ -104,7 +120,7 @@ export declare function handleRepl(): Promise<ExitCodeValue>;
 export declare function handleScaffold(sub: string | undefined, args: string[]): Promise<ExitCodeValue>;
 export declare function handleExplain(input: string | undefined): Promise<ExitCodeValue>;
 export declare function handleLearn(sub: string | undefined, args: string[]): Promise<ExitCodeValue>;
-export declare function handleSynthesis(sub: string | undefined, args: string[]): Promise<ExitCodeValue>;
+export declare function handleSynthesis(sub: string | undefined, args: string[], flags?: Record<string, unknown>): Promise<ExitCodeValue>;
 export declare function handleWatch(pattern: string | undefined): Promise<ExitCodeValue>;
 /**
  * Resolve the file/name target for a command, tolerating an optional leading
@@ -116,4 +132,5 @@ export declare function handleWatch(pattern: string | undefined): Promise<ExitCo
 export declare function resolveTarget(args: Record<string, unknown>, verbs: string[]): string | undefined;
 export declare function getDefaultCommands(): CLICommand[];
 export declare function createCLIDispatcher(): CLIDispatcher;
+export {};
 //# sourceMappingURL=cli.d.ts.map

package/dist/cli.d.ts.map

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package/dist/cli.js

@@ -12124,6 +12124,19 @@ var init_transport = __esm({
           this.rl = null;
         }
       }
+      /**
+       * Resolve once the input stream closes (client disconnect / stdin EOF).
+       * Used by the CLI launcher to keep the process alive for the lifetime of
+       * the connection — `start()` intentionally resolves immediately so callers
+       * can begin writing, so a separate wait hook is needed to block on.
+       */
+      async waitForClose() {
+        if (!this.rl)
+          return;
+        await new Promise((resolve9) => {
+          this.rl.once("close", () => resolve9());
+        });
+      }
       send(message) {
         this.output.write(JSON.stringify(message) + "\n");
       }
@@ -13989,7 +14002,7 @@ function knowledgeTools() {
         const { createKnowledgeStore: createKnowledgeStore2 } = await Promise.resolve().then(() => (init_dist8(), dist_exports8));
         const store = createKnowledgeStore2(params["basePath"] ?? ".knowledge");
         await store.load();
-        const entity = store.getEntity(params["id"]);
+        const entity = await store.getEntity(params["id"]);
         return entity ? ok(entity) : fail("Entity not found");
       } catch {
         return fail("Knowledge package not available");
@@ -14062,7 +14075,7 @@ function knowledgeTools() {
         const { createKnowledgeStore: createKnowledgeStore2 } = await Promise.resolve().then(() => (init_dist8(), dist_exports8));
         const store = createKnowledgeStore2(params["basePath"] ?? ".knowledge");
         await store.load();
-        const results = store.search(params["query"], { limit: params["limit"] ?? 10 });
+        const results = await store.search(params["query"], { limit: params["limit"] ?? 10 });
         return ok(results);
       } catch {
         return fail("Knowledge package not available");
@@ -14077,7 +14090,7 @@ function knowledgeTools() {
         const { createKnowledgeStore: createKnowledgeStore2 } = await Promise.resolve().then(() => (init_dist8(), dist_exports8));
         const store = createKnowledgeStore2(params["basePath"] ?? ".knowledge");
         await store.load();
-        const result = store.traverse(params["startId"], { depth: params["depth"] ?? 2 });
+        const result = await store.traverse(params["startId"], { depth: params["depth"] ?? 2 });
         return ok(result);
       } catch {
         return fail("Knowledge package not available");
@@ -14249,52 +14262,64 @@ function codeAnalysisTools() {
     })
   ];
 }
+function sourceOf(params) {
+  return params["code"] ?? params["source"] ?? params["target"] ?? "";
+}
+function severityOf(findings) {
+  const order = ["critical", "high", "medium", "low", "info"];
+  for (const s of order)
+    if (findings.some((f) => f.severity === s))
+      return s;
+  return "none";
+}
 function securityTools() {
   return [
     tool("security.scan", "Run a security scan on source code", "security", [
-      param("target", "string", "File or directory path to scan"),
-      param("rules", "array", "Specific rules to apply", false)
+      param("code", "string", "Source code to scan"),
+      param("filePath", "string", "File path for the source (for reporting)", false, "inline")
     ], async (params) => {
       try {
-        const sec = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
-        const result = sec.scan?.(params["target"], params["rules"]);
-        return ok(result ?? { findings: [], severity: "none" });
+        const { createSecurityScanner: createSecurityScanner2 } = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
+        const result = createSecurityScanner2().scan(sourceOf(params), params["filePath"] ?? "inline");
+        return ok({ findings: result.findings, severity: severityOf(result.findings) });
       } catch {
-        return ok({ findings: [], severity: "none" });
+        return fail("Security package not available");
       }
     }),
-    tool("security.secrets.detect", "Detect secrets and credentials in source code", "security", [param("target", "string", "File or directory path to scan")], async (params) => {
+    tool("security.secrets.detect", "Detect secrets and credentials in source code", "security", [
+      param("code", "string", "Source code to scan"),
+      param("filePath", "string", "File path for the source", false, "inline")
+    ], async (params) => {
       try {
-        const sec = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
-        const result = sec.detectSecrets?.(params["target"]);
-        return ok(result ?? { secrets: [], count: 0 });
+        const { createSecretDetector: createSecretDetector2 } = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
+        const secrets = createSecretDetector2().scan(sourceOf(params), params["filePath"] ?? "inline");
+        return ok({ secrets, count: secrets.length });
       } catch {
-        return ok({ secrets: [], count: 0 });
+        return fail("Security package not available");
       }
     }),
     tool("security.taint.analyze", "Perform taint analysis to track untrusted data flow", "security", [
-      param("source", "string", "Source code to analyze"),
-      param("sources", "array", "Taint sources", false),
-      param("sinks", "array", "Taint sinks", false)
+      param("code", "string", "Source code to analyze"),
+      param("filePath", "string", "File path for the source", false, "inline")
     ], async (params) => {
       try {
-        const sec = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
-        const result = sec.taintAnalysis?.(params["source"], params["sources"], params["sinks"]);
-        return ok(result ?? { tainted: [], paths: [] });
+        const { TaintAnalyzer: TaintAnalyzer2 } = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
+        const tainted = new TaintAnalyzer2().analyze(sourceOf(params), params["filePath"] ?? "inline");
+        return ok({ tainted, count: tainted.length });
       } catch {
-        return ok({ tainted: [], paths: [] });
+        return fail("Security package not available");
       }
     }),
-    tool("security.compliance.check", "Check code compliance against security standards", "security", [
-      param("target", "string", "File or directory path"),
-      param("standard", "string", "Compliance standard: owasp | cwe | sans", false, "owasp")
+    tool("security.compliance.check", "Check code compliance against registered security policies", "security", [
+      param("code", "string", "Source code to check"),
+      param("filePath", "string", "File path for the source", false, "inline")
     ], async (params) => {
       try {
-        const sec = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
-        const result = sec.complianceCheck?.(params["target"], params["standard"] ?? "owasp");
-        return ok(result ?? { compliant: true, issues: [] });
+        const { createComplianceChecker: createComplianceChecker2 } = await Promise.resolve().then(() => (init_dist5(), dist_exports5));
+        const result = createComplianceChecker2().check(sourceOf(params), params["filePath"] ?? "inline", []);
+        return ok(result);
       } catch {
-        return ok({ compliant: true, issues: [] });
+        return fail("Security package not available");
       }
     })
   ];
@@ -15307,6 +15332,7 @@ var init_mcp_cli_launcher = __esm({
         } else {
           const transport = new StdioTransport2();
           await server.start(transport);
+          await transport.waitForClose();
         }
       }
     };
@@ -15392,12 +15418,12 @@ var COMMAND_HELP = {
     description: "\u30BF\u30B9\u30AF\u7BA1\u7406"
   },
   trace: {
-    usage: "musubix trace <matrix|validate|impact> [args]",
-    description: "\u30C8\u30EC\u30FC\u30B5\u30D3\u30EA\u30C6\u30A3"
+    usage: "musubix trace <matrix|validate|impact> [--specs <file>] [--src <dir>]",
+    description: "\u30C8\u30EC\u30FC\u30B5\u30D3\u30EA\u30C6\u30A3\uFF08\u8981\u4EF6 \u2192 \u30B3\u30FC\u30C9\u306E REQ-ID \u53C2\u7167\u3092\u89E3\u6790\uFF09"
   },
   "trace:verify": {
-    usage: "musubix trace:verify",
-    description: "\u30C8\u30EC\u30FC\u30B5\u30D3\u30EA\u30C6\u30A3\u691C\u8A3C"
+    usage: "musubix trace:verify [--specs <file>] [--src <dir>] [--strict]",
+    description: "\u30C8\u30EC\u30FC\u30B5\u30D3\u30EA\u30C6\u30A3\u691C\u8A3C\uFF08\u672A\u53C2\u7167\u8981\u4EF6\u3092\u691C\u51FA\uFF09"
   },
   policy: {
     usage: "musubix policy <validate|list|info> [args]",
@@ -15412,7 +15438,7 @@ var COMMAND_HELP = {
     description: "\u30D7\u30ED\u30B8\u30A7\u30AF\u30C8\u72B6\u6CC1"
   },
   ontology: {
-    usage: "musubix ontology <validate|stats>",
+    usage: "musubix ontology <add|list|validate|stats> [args]",
     description: "\u30AA\u30F3\u30C8\u30ED\u30B8\u30FC\u7BA1\u7406"
   },
   cg: {
@@ -15684,13 +15710,68 @@ async function handleInit(targetPath = ".", name, force) {
   }
   return ExitCode.SUCCESS;
 }
-async function handleTrace(sub, args) {
+var REQ_ID_RE = /REQ-[A-Z]{3}-\d{3}/g;
+function buildCodeTraceData(specsFile, srcDir) {
+  const reqIds = [];
+  if (existsSync11(specsFile)) {
+    const content = readFileSync6(specsFile, "utf-8");
+    for (const line of content.split("\n")) {
+      const m = line.match(/^#{1,4}\s+(REQ-[A-Z]{3}-\d{3})\b/);
+      if (m)
+        reqIds.push(m[1]);
+    }
+    if (reqIds.length === 0) {
+      for (const m of content.matchAll(REQ_ID_RE))
+        reqIds.push(m[0]);
+    }
+  }
+  const requirementIds = [...new Set(reqIds)];
+  const reqSet = new Set(requirementIds);
+  const refsByReq = /* @__PURE__ */ new Map();
+  const fileSet = /* @__PURE__ */ new Set();
+  const links = [];
+  if (existsSync11(srcDir)) {
+    for (const file of collectFiles(srcDir, (ext) => ext in EXT_TO_LANG)) {
+      const code = readFileSync6(file, "utf-8");
+      const refs = /* @__PURE__ */ new Set();
+      for (const m of code.matchAll(REQ_ID_RE)) {
+        if (reqSet.has(m[0]))
+          refs.add(m[0]);
+      }
+      for (const reqId of refs) {
+        fileSet.add(file);
+        links.push({ source: reqId, target: file, verified: false });
+        const arr = refsByReq.get(reqId) ?? [];
+        arr.push(file);
+        refsByReq.set(reqId, arr);
+      }
+    }
+  }
+  return { requirementIds, fileIds: [...fileSet].sort(), links, refsByReq };
+}
+function resolveTraceInputs(flags) {
+  return {
+    specsFile: flags["specs"] ?? "storage/specs/requirements.md",
+    srcDir: flags["src"] ?? (existsSync11("src") ? "src" : ".")
+  };
+}
+async function handleTrace(sub, args, flags = {}) {
   switch (sub) {
     case "matrix": {
+      const { specsFile, srcDir } = resolveTraceInputs(flags);
+      const data = buildCodeTraceData(specsFile, srcDir);
+      if (data.requirementIds.length === 0) {
+        console.log(`No requirements found in ${specsFile} \u2014 nothing to trace.`);
+        console.log("\u2139 Pass --specs <file> to point at your requirements document.");
+        return ExitCode.SUCCESS;
+      }
       const generator = createMatrixGenerator();
-      const report = generator.generate([], [], []);
+      const report = generator.generate(data.requirementIds, data.fileIds, data.links);
       console.log(generator.toMarkdown(report));
-      console.log("\n\u2139 No traceability data loaded \u2014 matrix is empty (completeness is N/A).");
+      const covered = data.requirementIds.filter((r) => (data.refsByReq.get(r)?.length ?? 0) > 0);
+      const pct = Math.round(covered.length / data.requirementIds.length * 100);
+      console.log(`
+Requirements: ${data.requirementIds.length}, referenced in code: ${covered.length} (${pct}%), source files: ${data.fileIds.length} (scanned ${srcDir}).`);
       return ExitCode.SUCCESS;
     }
     case "validate": {
@@ -15719,23 +15800,27 @@ async function handleTrace(sub, args) {
       return ExitCode.SUCCESS;
   }
 }
-async function handleTraceVerify() {
-  const validator = createTraceabilityValidator();
-  const report = validator.validateCoverage([], [], [], []);
-  if (report.totalRequirements === 0) {
-    console.log("No traceability data loaded \u2014 nothing to verify.");
+async function handleTraceVerify(flags = {}) {
+  const { specsFile, srcDir } = resolveTraceInputs(flags);
+  const data = buildCodeTraceData(specsFile, srcDir);
+  if (data.requirementIds.length === 0) {
+    console.log(`No requirements found in ${specsFile} \u2014 nothing to verify.`);
     console.log("\u2139 Coverage cannot be computed with 0 requirements (reported as N/A).");
     return ExitCode.SUCCESS;
   }
-  console.log(`Coverage: ${report.coveragePercent}%`);
-  console.log(`Requirements: ${report.coveredRequirements}/${report.totalRequirements}`);
-  if (report.gaps.length > 0) {
-    console.log("Gaps:");
-    for (const gap of report.gaps) {
-      console.log(`  - ${JSON.stringify(gap)}`);
-    }
+  const covered = data.requirementIds.filter((r) => (data.refsByReq.get(r)?.length ?? 0) > 0);
+  const gaps = data.requirementIds.filter((r) => (data.refsByReq.get(r)?.length ?? 0) === 0);
+  const pct = Math.round(covered.length / data.requirementIds.length * 100);
+  console.log(`Coverage: ${pct}%`);
+  console.log(`Requirements: ${covered.length}/${data.requirementIds.length} referenced in ${srcDir}`);
+  if (gaps.length > 0) {
+    console.log("Gaps (requirements not referenced in code):");
+    for (const id of gaps)
+      console.log(`  - ${id}`);
+    if (flags["strict"] === true)
+      return ExitCode.VALIDATION_ERROR;
   } else {
-    console.log("No gaps found");
+    console.log("No gaps found \u2014 every requirement is referenced in code.");
   }
   return ExitCode.SUCCESS;
 }
@@ -15783,23 +15868,70 @@ async function handlePolicy(sub, args) {
       return ExitCode.SUCCESS;
   }
 }
-async function handleOntology(sub) {
+var ONTOLOGY_STATE_FILE = ".musubix/ontology.json";
+function loadOntologyStore() {
+  const store = createOntologyStore();
+  try {
+    if (existsSync11(ONTOLOGY_STATE_FILE)) {
+      const triples = JSON.parse(readFileSync6(ONTOLOGY_STATE_FILE, "utf-8"));
+      store.addTriples(triples);
+    }
+  } catch {
+  }
+  return store;
+}
+function saveOntologyStore(store) {
+  mkdirSync3(dirnamePath(ONTOLOGY_STATE_FILE), { recursive: true });
+  writeFileSync3(ONTOLOGY_STATE_FILE, JSON.stringify(store.getAll(), null, 2), "utf-8");
+}
+async function handleOntology(sub, args = []) {
   switch (sub) {
+    case "add": {
+      const [subject, predicate, object] = args;
+      if (!subject || !predicate || !object) {
+        console.error("\u274C Usage: musubix ontology add <subject> <predicate> <object>");
+        return ExitCode.VALIDATION_ERROR;
+      }
+      const store = loadOntologyStore();
+      store.addTriple({ subject, predicate, object });
+      saveOntologyStore(store);
+      console.log(`\u2705 Added triple: ${subject} \u2014[${predicate}]\u2192 ${object}`);
+      console.log(`   Total triples: ${store.size()}`);
+      return ExitCode.SUCCESS;
+    }
+    case "list": {
+      const store = loadOntologyStore();
+      const triples = store.getAll();
+      if (triples.length === 0) {
+        console.log("No triples stored yet. Add one with: musubix ontology add <s> <p> <o>");
+      } else {
+        console.log(`Triples (${triples.length}):`);
+        for (const t of triples) {
+          console.log(`  ${t.subject} \u2014[${t.predicate}]\u2192 ${t.object}`);
+        }
+      }
+      return ExitCode.SUCCESS;
+    }
     case "validate": {
-      const store = createOntologyStore();
+      const store = loadOntologyStore();
       const validator = createConsistencyValidator();
       const result = validator.validate(store);
-      console.log(`Consistent: ${result.consistent ? "\u2705" : "\u274C"}`);
+      if (store.size() === 0) {
+        console.log("No triples stored \u2014 nothing to validate.");
+        return ExitCode.SUCCESS;
+      }
+      console.log(`Consistent: ${result.consistent ? "\u2705" : "\u274C"} (${store.size()} triples)`);
       if (result.violations.length > 0) {
         console.log("Violations:");
         for (const v of result.violations) {
           console.log(`  - ${JSON.stringify(v)}`);
         }
+        return ExitCode.VALIDATION_ERROR;
       }
       return ExitCode.SUCCESS;
     }
     case "stats": {
-      const store = createOntologyStore();
+      const store = loadOntologyStore();
       console.log(`Triples: ${store.size()}`);
       return ExitCode.SUCCESS;
     }
@@ -16853,7 +16985,7 @@ async function handleLearn(sub, args) {
       return ExitCode.SUCCESS;
   }
 }
-async function handleSynthesis(sub, args) {
+async function handleSynthesis(sub, args, flags = {}) {
   switch (sub) {
     case "fromExamples": {
       const { createSynthesisEngine: createSynthesisEngine2 } = await Promise.resolve().then(() => (init_dist12(), dist_exports12));
@@ -16876,12 +17008,66 @@ async function handleSynthesis(sub, args) {
       const builder = createDSLBuilder2();
       const input = args[0];
       if (!input) {
-        console.error("\u274C Usage: musubix synthesis dsl <input>");
+        console.error("\u274C Usage: musubix synthesis dsl <input> --ops <op[:arg...],...>");
+        console.error("   ops: trim, upper, lower, reverse, capitalize, camelCase, snakeCase,");
+        console.error("        replace:from:to, prefixRemove:p, suffixAppend:s, repeat:n");
         return ExitCode.GENERAL_ERROR;
       }
+      const opsSpec = flags["ops"] ?? "";
+      const ops = opsSpec.split(",").map((o) => o.trim()).filter(Boolean);
+      if (ops.length === 0) {
+        console.error("\u274C No transforms given. Pass --ops <op,...> (e.g. --ops trim,camelCase).");
+        return ExitCode.VALIDATION_ERROR;
+      }
+      for (const op of ops) {
+        const [name, ...opArgs] = op.split(":");
+        switch (name) {
+          case "trim":
+            builder.trim();
+            break;
+          case "upper":
+          case "toUpperCase":
+            builder.toUpperCase();
+            break;
+          case "lower":
+          case "toLowerCase":
+            builder.toLowerCase();
+            break;
+          case "reverse":
+            builder.reverse();
+            break;
+          case "capitalize":
+            builder.capitalize();
+            break;
+          case "camelCase":
+          case "camel":
+            builder.camelCase();
+            break;
+          case "snakeCase":
+          case "snake":
+            builder.snakeCase();
+            break;
+          case "replace":
+            builder.replace(opArgs[0] ?? "", opArgs[1] ?? "");
+            break;
+          case "prefixRemove":
+            builder.prefixRemove(opArgs[0] ?? "");
+            break;
+          case "suffixAppend":
+            builder.suffixAppend(opArgs[0] ?? "");
+            break;
+          case "repeat":
+            builder.repeat(Number.parseInt(opArgs[0] ?? "1", 10) || 1);
+            break;
+          default:
+            console.error(`\u274C Unknown DSL op: ${name}`);
+            return ExitCode.VALIDATION_ERROR;
+        }
+      }
       const result = builder.execute(input);
       console.log(`DSL output:`);
-      console.log(`  Input: ${input}`);
+      console.log(`  Input:  ${input}`);
+      console.log(`  Ops:    ${ops.join(" \u2192 ")}`);
       console.log(`  Result: ${result}`);
       return ExitCode.SUCCESS;
     }
@@ -17154,7 +17340,7 @@ function getDefaultCommands() {
         }
         const sub = args["subcommand"];
         const positionalArgs = args["args"] ?? [];
-        return await handleTrace(sub, positionalArgs);
+        return await handleTrace(sub, positionalArgs, args);
       }
     },
     {
@@ -17165,7 +17351,7 @@ function getDefaultCommands() {
           console.log(showHelp("trace:verify"));
           return;
         }
-        return await handleTraceVerify();
+        return await handleTraceVerify(args);
       }
     },
     {
@@ -17190,7 +17376,8 @@ function getDefaultCommands() {
           return;
         }
         const sub = args["subcommand"];
-        return await handleOntology(sub);
+        const positionalArgs = args["args"] ?? [];
+        return await handleOntology(sub, positionalArgs);
       }
     },
     {
@@ -17359,7 +17546,7 @@ function getDefaultCommands() {
         }
         const sub = args["subcommand"];
         const positionalArgs = args["args"] ?? [];
-        return await handleSynthesis(sub, positionalArgs);
+        return await handleSynthesis(sub, positionalArgs, args);
       }
     },
     {
@@ -17409,6 +17596,7 @@ function createCLIDispatcher() {
 }
 export {
   CLIDispatcher,
+  buildCodeTraceData,
   collectFiles,
   createCLIDispatcher,
   getDefaultCommands,