@lamentis/naome 1.1.2 → 1.2.1

package/templates/naome-root/.naome/bin/naome.js

@@ -27,7 +27,7 @@ function main(argv) {
     return;
   }
 
-  if (command === "status" || command === "next" || command === "intent" || command === "route" || command === "explain") {
+  if (["status", "next", "intent", "route", "explain", "quality", "structure", "cleanup", "refresh-integrity", "workflow"].includes(command)) {
     runNativeDecisionCommand(command, args);
     return;
   }
@@ -46,20 +46,25 @@ function runNativeDecisionCommand(command, args) {
     fail("NAOME harness root not found. Run this inside a repository with .naome/task-state.json.");
   }
 
-  const nativeBinary = resolveNativeDecisionBinary(root);
-  verifyNativeBinary(nativeBinary);
+  const result = spawnNative(root, [command, ...args], { stdio: "inherit" });
+
+  process.exit(result.status === null ? 1 : result.status);
+}
 
-  const result = spawnSync(nativeBinary, [command, ...args], {
+function spawnNative(root, args, options = {}) {
+  const nativeBinary = resolveNativeDecisionBinary(root);
+  if (!isUsableNativeBinary(nativeBinary, root)) {
+    fail("NAOME native decision binary failed integrity or compatibility checks.");
+  }
+  return spawnSync(nativeBinary, args, {
     cwd: root,
     encoding: "utf8",
     env: {
       ...process.env,
       NAOME_NODE_BIN: process.execPath
     },
-    stdio: "inherit"
+    ...options
   });
-
-  process.exit(result.status === null ? 1 : result.status);
 }
 
 function resolveNativeDecisionBinary(root) {
@@ -115,30 +120,22 @@ function buildSourceNativeBinary(root) {
     return null;
   }
 
-  const manifestPath = join(root, "packages", "naome", "Cargo.toml");
+  const sourcePath = (...parts) => join(root, "packages", "naome", ...parts);
+  const manifestPath = sourcePath("Cargo.toml");
   if (!existsSync(manifestPath)) {
     return null;
   }
 
-  const result = spawnSync("cargo", ["build", "--release", "--manifest-path", manifestPath, "-p", "naome-cli"], {
-    cwd: root,
-    encoding: "utf8",
-    stdio: "ignore"
-  });
+  const buildArgs = ["build", "--release", "--manifest-path", manifestPath, "-p", "naome-cli"];
+  const result = spawnSync("cargo", buildArgs, { cwd: root, encoding: "utf8", stdio: "ignore" });
   if (result.status !== 0) {
     return null;
   }
 
-  const builtPath = join(root, "packages", "naome", "target", "release", nativeBinaryName);
+  const builtPath = sourcePath("target", "release", nativeBinaryName);
   return existsSync(builtPath) ? builtPath : null;
 }
 
-function verifyNativeBinary(nativeBinary) {
-  if (!isUsableNativeBinary(nativeBinary, findHarnessRoot(process.cwd()) || process.cwd())) {
-    fail("NAOME native decision binary failed integrity or compatibility checks.");
-  }
-}
-
 function commit(args) {
   const root = findHarnessRoot(process.cwd());
   if (!root) {
@@ -179,16 +176,7 @@ function commitBaseline(root, message, options = {}) {
 }
 
 function readTaskCommitPaths(root) {
-  const nativeBinary = resolveNativeDecisionBinary(root);
-  verifyNativeBinary(nativeBinary);
-  const result = spawnSync(nativeBinary, ["commit-paths", "--json"], {
-    cwd: root,
-    encoding: "utf8",
-    env: {
-      ...process.env,
-      NAOME_NODE_BIN: process.execPath
-    }
-  });
+  const result = spawnNative(root, ["commit-paths", "--json"]);
   if (result.status !== 0) {
     fail(`Cannot determine NAOME task commit paths: ${result.stderr.trim() || result.stdout.trim()}`);
   }
@@ -205,8 +193,6 @@ function readTaskCommitPaths(root) {
 }
 
 function writeTaskJournal(root, outcome, commitInfo) {
-  const nativeBinary = resolveNativeDecisionBinary(root);
-  verifyNativeBinary(nativeBinary);
   const args = [
     "journal-task",
     "--outcome",
@@ -220,14 +206,7 @@ function writeTaskJournal(root, outcome, commitInfo) {
     args.push("--commit-after", commitInfo.after);
   }
 
-  const result = spawnSync(nativeBinary, args, {
-    cwd: root,
-    encoding: "utf8",
-    env: {
-      ...process.env,
-      NAOME_NODE_BIN: process.execPath
-    }
-  });
+  const result = spawnNative(root, args);
   if (result.status !== 0) {
     fail(`Cannot write NAOME task journal: ${result.stderr.trim() || result.stdout.trim()}`);
   }
@@ -261,16 +240,7 @@ function defaultSetupCommitMessage(decision) {
 }
 
 function readDecision(root) {
-  const nativeBinary = resolveNativeDecisionBinary(root);
-  verifyNativeBinary(nativeBinary);
-  const result = spawnSync(nativeBinary, ["status", "--json"], {
-    cwd: root,
-    encoding: "utf8",
-    env: {
-      ...process.env,
-      NAOME_NODE_BIN: process.execPath
-    }
-  });
+  const result = spawnNative(root, ["status", "--json"]);
 
   if (result.status !== 0) {
     fail(`Cannot read NAOME status: ${result.stderr.trim() || result.stdout.trim()}`);
@@ -358,10 +328,14 @@ function gitHead(root) {
 }
 
 function findHarnessRoot(startPath) {
+  return findAncestorWithMarker(startPath, [".naome", "task-state.json"]);
+}
+
+function findAncestorWithMarker(startPath, markerParts) {
   let current = resolve(startPath);
 
   while (true) {
-    if (existsSync(join(current, ".naome", "task-state.json"))) {
+    if (existsSync(join(current, ...markerParts))) {
       return current;
     }
 
@@ -375,19 +349,30 @@ function findHarnessRoot(startPath) {
 }
 
 function printHelp() {
-  console.log("Usage:");
-  console.log("  naome status [--json]");
-  console.log("  naome next [--json]");
-  console.log("  naome intent --prompt-file <path> [--json]");
-  console.log("  naome intent --prompt <text> [--json]");
-  console.log("  naome route --prompt-file <path> [--execute] [--json]");
-  console.log("  naome route --prompt <text> [--execute] [--json]");
-  console.log("  naome explain --prompt-file <path> [--json]");
-  console.log("  naome explain --prompt <text> [--json]");
-  console.log("  naome install");
-  console.log("  naome sync");
-  console.log("  naome commit -m \"type(scope): message\"");
-  console.log("  node .naome/bin/naome.js commit -m \"type(scope): message\"");
+  const commands = [
+    "naome status [--json]",
+    "naome next [--json]",
+    "naome intent --prompt-file <path> [--json]",
+    "naome intent --prompt <text> [--json]",
+    "naome route --prompt-file <path> [--execute] [--json]",
+    "naome route --prompt <text> [--execute] [--json]",
+    "naome explain --prompt-file <path> [--json]",
+    "naome explain --prompt <text> [--json]",
+    "naome quality init [--json]",
+    "naome quality check --changed [--json]",
+    "naome quality report [--json]",
+    "naome structure report [--json]",
+    "naome structure explain --path <path> [--json]",
+    "naome cleanup plan [--json]",
+    "naome cleanup route --path <path> [--json]",
+    "naome refresh-integrity [--json]",
+    "naome workflow search-profile|check-search|phases|processes|mutations [--json]",
+    "naome install",
+    "naome sync",
+    "naome commit -m \"type(scope): message\"",
+    "node .naome/bin/naome.js commit -m \"type(scope): message\""
+  ];
+  console.log(["Usage:", ...commands.map((command) => `  ${command}`)].join("\n"));
 }
 
 function fail(message) {
@@ -399,24 +384,14 @@ function installOrSync(command, args) {
   const root = findHarnessRoot(process.cwd()) || process.cwd();
   const packageRoot = sourcePackageRoot(root);
   if (packageRoot) {
-    const nativeBinary = resolveNativeDecisionBinary(root);
-    verifyNativeBinary(nativeBinary);
-    const result = spawnSync(nativeBinary, [
+    const result = spawnNative(root, [
       command,
       "--package-root",
       packageRoot,
       "--installer-js",
       join(packageRoot, "bin", "naome-node.js"),
       ...args
-    ], {
-      cwd: root,
-      encoding: "utf8",
-      env: {
-        ...process.env,
-        NAOME_NODE_BIN: process.execPath
-      },
-      stdio: "inherit"
-    });
+    ], { stdio: "inherit" });
     process.exit(result.status === null ? 1 : result.status);
   }
 

package/templates/naome-root/.naome/manifest.json

@@ -1,8 +1,19 @@
 {
-  "name": "naome",
-  "harnessVersion": "1.1.1",
-  "profile": "standard",
+  "harnessVersion": "1.2.0",
   "installedAt": null,
+  "integrity": {
+    ".naome/bin/check-harness-health.js": "sha256:dc4de52b79c69600b9ba47b924e2c2b8de61a2cbfab6d1ccc0f1924d963db657",
+    ".naome/bin/check-task-state.js": "sha256:43c02868072d0d13499aefba2e9a5ec9517d59539fd19ff0f11e3e4623a51b44",
+    ".naome/bin/naome.js": "sha256:87eabd690bf55f0b0195446db46fa7c19bfa17395d31c2f34a9ef9339d2229e2",
+    ".naome/package.json": "sha256:8005a3491db7d92f36ac66369861589f9c47123d3a7c71e643fc2c06168cd45a",
+    ".naome/task-contract.schema.json": "sha256:1b3b62350328d0d6d660e36d1d1baaa2b88718530db774f9ab2a9e2fcba369c8",
+    "AGENTS.md": "sha256:9192ea81f90bb19f8043513c49b5da9e9598ee694da8356f345e7ccbca0e28df",
+    "docs/naome/agent-workflow.md": "sha256:802eb34cf268fc9c5e7aefc28192efef4bf60302d30b3f78e5a61b876ce8a098",
+    "docs/naome/execution.md": "sha256:bfc5d55838942ec8e3d790b59e3c634ff5bf6a2298265cef3dca9788a097eafb",
+    "docs/naome/first-run.md": "sha256:a1dd0bd17ec9d71955a473cd2c4a615538e89a7d81e8f4e1015a50ab9efe3558",
+    "docs/naome/index.md": "sha256:a674102cc801702dc77102afb59be0f5ab189dc638caf0bef358b9d6087d0742",
+    "docs/naome/upgrade.md": "sha256:2c60f0441bbd98bd528d109b30a7ded4b0ad55d61ffb9f52edac9e93b7999cb1"
+  },
   "machineOwned": [
     "AGENTS.md",
     ".naome/package.json",
@@ -16,6 +27,8 @@
     "docs/naome/execution.md",
     "docs/naome/upgrade.md"
   ],
+  "name": "naome",
+  "profile": "standard",
   "projectOwned": [
     ".naomeignore",
     ".naome/init-state.json",
@@ -23,24 +36,15 @@
     ".naome/task-state.json",
     ".naome/upgrade-state.json",
     ".naome/verification.json",
+    ".naome/repository-quality.json",
+    ".naome/repository-structure.json",
+    ".naome/repository-quality-baseline.json",
     "docs/naome/architecture.md",
     "docs/naome/decisions.md",
     "docs/naome/repo-profile.md",
+    "docs/naome/repository-quality.md",
+    "docs/naome/repository-structure.md",
     "docs/naome/security.md",
     "docs/naome/testing.md"
-  ],
-  "integrity": {
-    "AGENTS.md": "sha256:84ce882fa6798a144c8c74673d4304fc6bf235b1cc417f7649eea9f7461775de",
-    ".naome/package.json": "sha256:8005a3491db7d92f36ac66369861589f9c47123d3a7c71e643fc2c06168cd45a",
-    ".naome/bin/naome.js": "sha256:7894690ad47700a9a5e7ecb5a94ba42c1a12e2637d2c9f41f0023b1bd8bd22b6",
-    ".naome/bin/check-task-state.js": "sha256:43c02868072d0d13499aefba2e9a5ec9517d59539fd19ff0f11e3e4623a51b44",
-    ".naome/bin/check-harness-health.js": "sha256:dce2a380022dd63d86bd762869debafbc635ab3d7e8fae985e2d429d8ee437ad",
-    ".naome/task-contract.schema.json": "sha256:c806416d4944eaed6dc48b3760fd0dd5b9b5a7c9ab895697fe36b54c41c1332f",
-    "docs/naome/index.md": "sha256:d04691b25ed377c2a3aa2c56965d0db276539aeadcfdd2a2ec1be7ff7706dd6f",
-    "docs/naome/first-run.md": "sha256:a1dd0bd17ec9d71955a473cd2c4a615538e89a7d81e8f4e1015a50ab9efe3558",
-    "docs/naome/agent-workflow.md": "sha256:43ba8a6814068e1b932b12a392de70b39841dc82df0acdaac459d6714c501b9d",
-    "docs/naome/execution.md": "sha256:ad66611b2878d1ba8fe05ddc4cfe9de7fd41de172a0de8295c36227a2700631a",
-    "docs/naome/upgrade.md": "sha256:2c60f0441bbd98bd528d109b30a7ded4b0ad55d61ffb9f52edac9e93b7999cb1",
-    ".naome/bin/naome-rust": "sha256:cc754ae59477577dfc0130cc21c286beaf3f19e2852278bb8f1e8724277eb44b"
-  }
+  ]
 }

package/templates/naome-root/.naome/repository-quality-baseline.json

@@ -0,0 +1,5 @@
+{
+  "schema": "naome.repository-quality-baseline.v1",
+  "version": 1,
+  "violations": []
+}

package/templates/naome-root/.naome/repository-quality.json

@@ -0,0 +1,24 @@
+{
+  "schema": "naome.repository-quality.v1",
+  "version": 1,
+  "status": "ready",
+  "limits": {
+    "maxFileLines": 450,
+    "maxNewFileLines": 300,
+    "maxDiffAddedLines": 180,
+    "maxFunctionLines": 100,
+    "maxTopLevelSymbols": 30,
+    "duplicateBlockLines": 10,
+    "nearDuplicateSimilarity": 0.9
+  },
+  "enabledAdapters": [],
+  "disabledChecks": [],
+  "ignoredPaths": [],
+  "generatedPaths": [
+    "**/*.min.js",
+    "**/*.map",
+    "**/dist/**",
+    "**/build/**"
+  ],
+  "pathRules": []
+}

package/templates/naome-root/.naome/repository-structure.json

@@ -0,0 +1,90 @@
+{
+  "schema": "naome.repository-structure.v1",
+  "version": 1,
+  "status": "ready",
+  "enabledAdapters": [],
+  "sourceRoots": [
+    "src/**",
+    "app/**",
+    "apps/*/src/**",
+    "packages/*/src/**",
+    "crates/*/src/**",
+    "**/src/**",
+    "lib/**"
+  ],
+  "testRoots": [
+    "test/**",
+    "tests/**",
+    "__tests__/**",
+    "packages/*/test/**",
+    "packages/*/tests/**",
+    "crates/*/tests/**",
+    "**/tests/**",
+    "scripts/*.test.js"
+  ],
+  "docsRoots": [
+    "docs/**",
+    "doc/**"
+  ],
+  "generatedRoots": [
+    "**/generated/**",
+    "**/__generated__/**",
+    "**/codegen/**",
+    "**/*.generated.*"
+  ],
+  "artifactRoots": [
+    "dist/**",
+    "build/**",
+    "coverage/**",
+    ".next/**",
+    "target/**",
+    "**/dist/**",
+    "**/build/**"
+  ],
+  "moduleRoots": [
+    "src/**",
+    "app/**",
+    "packages/*/src/**",
+    "crates/*/src/**",
+    "**/src/**"
+  ],
+  "allowedRootFiles": [
+    "README.md",
+    "LICENSE",
+    "NOTICE",
+    "CHANGELOG.md",
+    "CONTRIBUTING.md",
+    "SECURITY.md",
+    "AGENTS.md",
+    "package.json",
+    "Cargo.toml",
+    "pyproject.toml",
+    "go.mod",
+    "go.sum",
+    "Makefile",
+    ".gitignore",
+    ".naomeignore"
+  ],
+  "directoryRoleRules": [],
+  "layerRules": [],
+  "ignoredPaths": [
+    ".git/**",
+    "node_modules/**",
+    "vendor/**",
+    "target/**",
+    "**/target/**",
+    "dist/**",
+    "build/**",
+    "coverage/**",
+    ".next/**"
+  ],
+  "disabledChecks": [],
+  "changedCodePolicy": "block",
+  "debtPolicy": "report",
+  "limits": {
+    "maxDirectoryFiles": 40,
+    "maxPathDepth": 10,
+    "maxDirectoryRoles": 2,
+    "maxDumpingGroundFiles": 12
+  }
+}

package/templates/naome-root/.naome/task-contract.schema.json

@@ -1,13 +1,13 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "naome.task-state.v1",
+  "$id": "naome.task-state.v2",
   "title": "NAOME Task State",
   "type": "object",
   "additionalProperties": false,
   "required": ["schema", "version", "status", "activeTask", "blocker", "updatedAt"],
   "properties": {
-    "schema": { "const": "naome.task-state.v1" },
-    "version": { "const": 1 },
+    "schema": { "enum": ["naome.task-state.v1", "naome.task-state.v2"] },
+    "version": { "enum": [1, 2] },
     "status": {
       "enum": ["idle", "planning", "implementing", "revising", "verifying", "needs_human_review", "blocked", "complete"]
     },
@@ -30,11 +30,29 @@
       ]
     }
   },
+  "oneOf": [
+    {
+      "properties": {
+        "schema": { "const": "naome.task-state.v1" },
+        "version": { "const": 1 }
+      }
+    },
+    {
+      "properties": {
+        "schema": { "const": "naome.task-state.v2" },
+        "version": { "const": 2 }
+      }
+    }
+  ],
   "$defs": {
     "activeTask": {
       "type": "object",
       "additionalProperties": false,
-      "required": ["id", "request", "userPrompt", "admission", "allowedPaths", "declaredChangeTypes", "requiredCheckIds", "proofResults", "humanReview"],
+      "required": ["id", "request", "userPrompt", "admission", "allowedPaths", "declaredChangeTypes", "requiredCheckIds", "humanReview"],
+      "anyOf": [
+        { "required": ["proofResults"] },
+        { "required": ["proofBatches"] }
+      ],
       "properties": {
         "id": { "type": "string", "pattern": "^[a-z0-9][a-z0-9-]*$" },
         "request": { "type": "string", "minLength": 1 },
@@ -58,6 +76,14 @@
           "type": "array",
           "items": { "$ref": "#/$defs/proofResult" }
         },
+        "proofPathSets": {
+          "type": "object",
+          "additionalProperties": { "$ref": "#/$defs/evidenceArray" }
+        },
+        "proofBatches": {
+          "type": "array",
+          "items": { "$ref": "#/$defs/proofBatch" }
+        },
         "revisions": {
           "type": "array",
           "items": { "$ref": "#/$defs/revision" }
@@ -109,17 +135,73 @@
         "cwd": { "type": "string", "minLength": 1 },
         "exitCode": { "type": "integer" },
         "checkedAt": { "type": "string", "format": "date-time" },
-        "evidence": {
+        "evidence": { "$ref": "#/$defs/evidenceArray" },
+        "outputSummary": { "$ref": "#/$defs/outputSummary" }
+      }
+    },
+    "proofBatch": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["checkedAt", "proofs"],
+      "properties": {
+        "checkedAt": { "type": "string", "format": "date-time" },
+        "command": { "type": "string", "minLength": 1 },
+        "cwd": { "type": "string", "minLength": 1 },
+        "evidencePathSet": { "type": "string", "minLength": 1 },
+        "proofs": {
+          "type": "array",
+          "items": { "$ref": "#/$defs/compactProofResult" }
+        }
+      }
+    },
+    "compactProofResult": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["checkId", "exitCode"],
+      "properties": {
+        "checkId": { "type": "string", "minLength": 1 },
+        "command": { "type": "string", "minLength": 1 },
+        "cwd": { "type": "string", "minLength": 1 },
+        "exitCode": { "type": "integer" },
+        "checkedAt": { "type": "string", "format": "date-time" },
+        "evidence": { "$ref": "#/$defs/evidenceArray" },
+        "evidencePathSet": { "type": "string", "minLength": 1 },
+        "outputSummary": { "$ref": "#/$defs/outputSummary" }
+      }
+    },
+    "outputSummary": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["command", "cwd", "exitCode", "truncated", "relevantLines", "affectedPaths"],
+      "properties": {
+        "command": { "type": "string", "minLength": 1 },
+        "cwd": { "type": "string", "minLength": 1 },
+        "exitCode": { "type": "integer" },
+        "truncated": { "type": "boolean" },
+        "omittedLineCount": { "type": "integer", "minimum": 0 },
+        "relevantLines": {
           "type": "array",
-          "items": {
-            "anyOf": [
-              { "type": "string", "minLength": 1 },
-              { "$ref": "#/$defs/evidenceEntry" }
-            ]
-          }
+          "items": { "type": "string" }
+        },
+        "affectedPaths": {
+          "type": "array",
+          "items": { "type": "string", "minLength": 1 }
+        },
+        "artifacts": {
+          "type": "array",
+          "items": { "type": "string", "minLength": 1 }
         }
       }
     },
+    "evidenceArray": {
+      "type": "array",
+      "items": {
+        "anyOf": [
+          { "type": "string", "minLength": 1 },
+          { "$ref": "#/$defs/evidenceEntry" }
+        ]
+      }
+    },
     "evidenceEntry": {
       "type": "object",
       "additionalProperties": false,

package/templates/naome-root/.naome/upgrade-state.json

@@ -1,7 +1,7 @@
 {
   "status": "complete",
   "fromVersion": null,
-  "toVersion": "1.1.1",
+  "toVersion": "1.2.0",
   "pending": [],
   "completed": []
 }

package/templates/naome-root/.naome/verification.json

@@ -38,6 +38,44 @@
         ".naome/task-contract.schema.json"
       ],
       "lastVerified": null
+    },
+    {
+      "id": "repository-quality-check",
+      "command": "node .naome/bin/naome.js quality check --changed",
+      "cwd": ".",
+      "purpose": "Validate changed files against deterministic NAOME repository quality rules.",
+      "cost": "fast",
+      "source": "NAOME built-in",
+      "evidence": [
+        ".naome/repository-quality.json",
+        ".naome/repository-structure.json",
+        ".naome/repository-quality-baseline.json"
+      ],
+      "lastVerified": null
+    }
+  ],
+  "phases": [
+    {
+      "id": "shape-health",
+      "order": 10,
+      "checkIds": [
+        "naome-harness-health",
+        "naome-task-state"
+      ]
+    },
+    {
+      "id": "quality",
+      "order": 20,
+      "checkIds": [
+        "repository-quality-check"
+      ]
+    },
+    {
+      "id": "diff-check",
+      "order": 60,
+      "checkIds": [
+        "diff-check"
+      ]
     }
   ],
   "changeTypes": [],

package/templates/naome-root/AGENTS.md

@@ -69,6 +69,9 @@ This repository uses NAOME as its coding-agent harness.
   previous-task, or other unowned changes.
 - Treat `.naomeignore` as a hard read boundary. Do not inspect ignored paths
   unless the user first removes the path from `.naomeignore`.
+- Use `naome workflow search-profile` or equivalent excludes for broad searches;
+  hidden searches must exclude `.git`, `.naome/archive`, dependencies, build
+  outputs, caches, and `.naomeignore` paths.
 - Use `docs/naome/testing.md` and `.naome/verification.json` before claiming
   completion.
 - Before claiming completion, run the narrowest meaningful verification that can