instrux 0.1.0 → 0.3.0

package/LICENSE-APACHE

@@ -0,0 +1,13 @@
+Copyright 2026 Travis Sharp
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

package/LICENSE-MIT

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Travis Sharp
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -39,6 +39,7 @@ instrux build MyAgent
 |---|---|
 | `instrux init <name>` | Scaffold a simple-merge agent |
 | `instrux init -t <name>` | Scaffold a template-compiled agent |
+| `instrux config:init` | Create repository-level config file |
 | `instrux build <name>` | Build (merge or compile) an agent |
 | `instrux build --all` | Build all agents |
 | `instrux list` | List all agents |
@@ -47,6 +48,114 @@ instrux build MyAgent
 
 ---
 
+## Repository Configuration
+
+A repository-level config file (`instrux.json`) at your project root sets default settings for all agents.
+
+**Auto-creation:** When you run `instrux init` for the first time, the repository config is created automatically with sensible defaults.
+
+You can also create it manually:
+
+```bash
+instrux config:init
+```
+
+This creates an `instrux.json` file with default settings:
+
+```json
+{
+  "agentsDirectory": "agents",
+  "outputDirectory": "out",
+  "mergeSettings": {
+    "addSeparators": true,
+    "separatorStyle": "---",
+    "includeFileHeaders": false,
+    "preserveFormatting": true,
+    "generateHash": false,
+    "useTimestamp": false
+  },
+  "frontmatter": {
+    "output": "strip"
+  },
+  "sources": ["agents/base/**/*.md"]
+}
+```
+
+**Configuration Options:**
+
+| Field | Default | Description |
+|---|---|---|
+| `agentsDirectory` | `"agents"` | Directory containing agent folders (e.g., `"src/agents"` for src/agents/MyAgent/) |
+| `outputDirectory` | `"out"` | Where to write compiled output files |
+| `mergeSettings` | See above | Default merge behavior for all agents |
+| `frontmatter` | `{ output: "strip" }` | How to handle frontmatter in output |
+| `sources` | `["agents/base/**/*.md"]` | Default source patterns for template mode |
+
+**Benefits:**
+- Set defaults once for all agents
+- Individual agent configs inherit these settings
+- Agent configs can override any setting
+- Keep agent configs minimal and focused
+
+**Example workflow:**
+
+```bash
+# 1. Create your first agent (auto-creates instrux.json)
+instrux init MyAgent
+
+# 2. (Optional) Edit instrux.json to customize defaults
+
+# 3. Create more agents - they inherit repo defaults
+instrux init AnotherAgent
+
+# 4. Agent configs only need to specify what's unique
+```
+
+**Using a custom agents directory:**
+
+To organize agents in a different location (e.g., `src/agents`):
+
+```bash
+# 1. Create instrux.json first
+instrux config:init
+
+# 2. Edit instrux.json and change agentsDirectory
+# {
+#   "agentsDirectory": "src/agents",
+#   ...
+# }
+
+# 3. Now create agents - they'll be in src/agents/
+instrux init MyAgent
+# Creates: src/agents/MyAgent/agent.json
+```
+
+**Config inheritance and precedence:**
+
+Settings are merged in this order (later overrides earlier):
+1. Built-in defaults (`DEFAULT_MERGE_SETTINGS`)
+2. Repository config (`instrux.json`)
+3. Agent config (`agents/<name>/agent.json`)
+
+This means:
+- If a setting is in the agent config, it's used
+- Otherwise, if it's in the repo config, it's used
+- Otherwise, the built-in default is used
+
+You can make agent configs minimal by removing fields you want to inherit:
+
+```json
+{
+  "name": "MyAgent",
+  "description": "My agent",
+  "files": [...]
+  // outputDirectory inherited from instrux.json
+  // mergeSettings inherited from instrux.json
+}
+```
+
+---
+
 ## Simple Mode (v1)
 
 Files are merged in the order listed in `agent.json`:
@@ -269,6 +378,46 @@ const compiler = new InstruxCompiler(process.cwd(), config);
 const { output, filesCompiled, tagsUsed } = await compiler.compile();
 ```
 
+## Development
+
+### Running Tests
+
+This project uses Jest for testing:
+
+```bash
+# Run all tests
+npm test
+
+# Run tests in watch mode
+npm run test:watch
+
+# Run tests with coverage
+npm run test:coverage
+```
+
+### Building
+
+```bash
+# Build TypeScript to JavaScript
+npm run build
+
+# Watch mode for development
+npm run watch
+```
+
+### Project Structure
+
+```
+src/
+  cli.ts           # CLI entry point
+  engine.ts        # Core build engine
+  compiler.ts      # Template compiler
+  init.ts          # Scaffolding functions
+  frontmatter.ts   # Frontmatter parsing
+  types.ts         # TypeScript types
+  *.test.ts        # Jest test files
+```
+
 ## License
 
 This project is dual-licensed under your choice of:

package/dist/cli.d.ts

@@ -4,6 +4,7 @@
  *
  * Commands:
  *   instrux init <name>       Scaffold a new agent
+ *   instrux config:init       Create repository-level config
  *   instrux build <name>      Merge instruction files for an agent
  *   instrux build --all       Build all agents
  *   instrux list              List available agents

package/dist/cli.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAEA;;;;;;;;;;GAUG"}
+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAEA;;;;;;;;;;;GAWG"}

package/dist/cli.js

@@ -5,16 +5,69 @@
  *
  * Commands:
  *   instrux init <name>       Scaffold a new agent
+ *   instrux config:init       Create repository-level config
  *   instrux build <name>      Merge instruction files for an agent
  *   instrux build --all       Build all agents
  *   instrux list              List available agents
  *   instrux config <name>     Show agent configuration
  *   instrux validate <name>   Validate source files exist
  */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 const commander_1 = require("commander");
+const path = __importStar(require("path"));
+const fs = __importStar(require("fs-extra"));
 const engine_1 = require("./engine");
 const init_1 = require("./init");
+/**
+ * Load repo config to get agentsDirectory for help text.
+ */
+async function getAgentsDir(rootDir) {
+    const configPath = path.join(rootDir, 'instrux.json');
+    if (await fs.pathExists(configPath)) {
+        try {
+            const raw = await fs.readFile(configPath, 'utf-8');
+            const config = JSON.parse(raw);
+            return config.agentsDirectory ?? 'agents';
+        }
+        catch {
+            return 'agents';
+        }
+    }
+    return 'agents';
+}
 const pkg = require('../package.json');
 const program = new commander_1.Command();
 program
@@ -33,20 +86,26 @@ program
             ? await (0, init_1.initTemplateAgent)(cwd, name)
             : await (0, init_1.initAgent)(cwd, name);
         const mode = opts.template ? 'template' : 'simple';
+        const isFirstAgent = created.includes('instrux.json');
+        const agentsDir = await getAgentsDir(cwd);
         console.log(`\n\u2705 Agent "${name}" initialized (${mode} mode)!\n`);
+        if (isFirstAgent) {
+            console.log('Created repository config (instrux.json) with default settings.');
+            console.log('This provides defaults for all agents in the project.\n');
+        }
         console.log('Created:');
         created.forEach(f => console.log(`  ${f}`));
         if (opts.template) {
             console.log(`\nNext steps:`);
-            console.log(`  1. Edit agents/base/*.md to define shared instructions`);
-            console.log(`  2. Edit agents/${name}/domain.md with domain knowledge`);
-            console.log(`  3. Edit agents/${name}/template.md to compose via {{tag "..."}}`);
+            console.log(`  1. Edit ${agentsDir}/base/*.md to define shared instructions`);
+            console.log(`  2. Edit ${agentsDir}/${name}/domain.md with domain knowledge`);
+            console.log(`  3. Edit ${agentsDir}/${name}/template.md to compose via {{tag "..."}}`);
             console.log(`  4. Run: instrux build ${name}\n`);
         }
         else {
             console.log(`\nNext steps:`);
-            console.log(`  1. Edit agents/${name}/specialization.md with your instructions`);
-            console.log(`  2. Edit agents/${name}/agent.json to add more files if needed`);
+            console.log(`  1. Edit ${agentsDir}/${name}/specialization.md with your instructions`);
+            console.log(`  2. Edit ${agentsDir}/${name}/agent.json to add more files if needed`);
             console.log(`  3. Run: instrux build ${name}\n`);
         }
     }
@@ -55,6 +114,30 @@ program
         process.exit(1);
     }
 });
+// ── config:init ────────────────────────────────────────────
+program
+    .command('config:init')
+    .description('Create a repository-level config file (instrux.json)')
+    .action(async () => {
+    try {
+        const cwd = process.cwd();
+        const created = await (0, init_1.initRepoConfig)(cwd);
+        console.log(`\n✅ Repository config created!\n`);
+        console.log(`Created: ${created}\n`);
+        console.log('This file provides default settings for all agents.');
+        console.log('Individual agent configs will inherit and can override these settings.\n');
+        console.log('Default settings:');
+        console.log('  - agentsDirectory: "agents"');
+        console.log('  - outputDirectory: "out"');
+        console.log('  - mergeSettings: standard defaults');
+        console.log('  - frontmatter: { output: "strip" }');
+        console.log('  - sources: ["agents/base/**/*.md"]\n');
+    }
+    catch (err) {
+        console.error(`❌ ${err.message}`);
+        process.exit(1);
+    }
+});
 // ── build ──────────────────────────────────────────────────
 program
     .command('build [name]')
@@ -109,10 +192,17 @@ program
     console.log('\nAvailable agents:\n');
     for (const agent of agents) {
         if (agent.config) {
-            const mode = agent.config.entry ? 'template' : 'simple';
-            console.log(`  ${agent.name}  [${mode}]`);
-            console.log(`    ${agent.config.description}`);
-            console.log(`    Files: ${agent.config.files?.length ?? agent.config.sources?.length ?? 0}  \u2192  ${agent.config.outputDirectory}/${agent.config.outputFilePattern}`);
+            try {
+                // Load full resolved config to get all values with defaults
+                const resolved = await engine.loadConfig(agent.name);
+                const mode = resolved.entry ? 'template' : 'simple';
+                console.log(`  ${agent.name}  [${mode}]`);
+                console.log(`    ${resolved.description}`);
+                console.log(`    Files: ${resolved.files?.length ?? resolved.sources?.length ?? 0}  \u2192  ${resolved.outputDirectory}/${resolved.outputFilePattern}`);
+            }
+            catch (err) {
+                console.log(`  ${agent.name}  (error loading config)`);
+            }
         }
         else {
             console.log(`  ${agent.name}  (invalid or missing agent.json)`);
@@ -140,9 +230,13 @@ program
         });
         console.log();
         console.log('  Merge settings:');
-        Object.entries(config.mergeSettings).forEach(([k, v]) => {
-            console.log(`    ${k}: ${v}`);
-        });
+        const ms = config.mergeSettings;
+        console.log(`    addSeparators: ${ms.addSeparators}`);
+        console.log(`    separatorStyle: ${ms.separatorStyle}`);
+        console.log(`    includeFileHeaders: ${ms.includeFileHeaders}`);
+        console.log(`    preserveFormatting: ${ms.preserveFormatting}`);
+        console.log(`    generateHash: ${ms.generateHash}`);
+        console.log(`    useTimestamp: ${ms.useTimestamp}`);
         console.log();
     }
     catch (err) {

package/dist/cli.js.map

@@ -1 +1 @@
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package/dist/compiler.d.ts

@@ -11,7 +11,7 @@
  *   4. Cycle detection via a compile stack
  *   5. Emit final output with optional frontmatter passthrough
  */
-import { AgentConfig } from './types';
+import { ResolvedAgentConfig } from './types';
 export interface CompileResult {
     /** Final compiled output (may include frontmatter block) */
     output: string;
@@ -27,7 +27,7 @@ export declare class InstruxCompiler {
     private compileStack;
     private compiledFiles;
     private tagsUsed;
-    constructor(rootDir: string, config: AgentConfig);
+    constructor(rootDir: string, config: ResolvedAgentConfig);
     compile(): Promise<CompileResult>;
     private compileFile;
     private registerHelpers;

package/dist/compiler.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"compiler.d.ts","sourceRoot":"","sources":["../src/compiler.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAMH,OAAO,EACL,WAAW,EAIZ,MAAM,SAAS,CAAC;AAQjB,MAAM,WAAW,aAAa;IAC5B,4DAA4D;IAC5D,MAAM,EAAE,MAAM,CAAC;IACf,gDAAgD;IAChD,aAAa,EAAE,MAAM,CAAC;IACtB,mDAAmD;IACnD,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,qBAAa,eAAe;IAC1B,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,MAAM,CAAc;IAC5B,OAAO,CAAC,KAAK,CAAe;IAC5B,OAAO,CAAC,YAAY,CAA0B;IAC9C,OAAO,CAAC,aAAa,CAA0B;IAC/C,OAAO,CAAC,QAAQ,CAA0B;gBAE9B,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW;IAO1C,OAAO,IAAI,OAAO,CAAC,aAAa,CAAC;IAgDvC,OAAO,CAAC,WAAW;IA+CnB,OAAO,CAAC,eAAe;CA2ExB"}
+{"version":3,"file":"compiler.d.ts","sourceRoot":"","sources":["../src/compiler.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAMH,OAAO,EAEL,mBAAmB,EAIpB,MAAM,SAAS,CAAC;AAQjB,MAAM,WAAW,aAAa;IAC5B,4DAA4D;IAC5D,MAAM,EAAE,MAAM,CAAC;IACf,gDAAgD;IAChD,aAAa,EAAE,MAAM,CAAC;IACtB,mDAAmD;IACnD,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,qBAAa,eAAe;IAC1B,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,MAAM,CAAsB;IACpC,OAAO,CAAC,KAAK,CAAe;IAC5B,OAAO,CAAC,YAAY,CAA0B;IAC9C,OAAO,CAAC,aAAa,CAA0B;IAC/C,OAAO,CAAC,QAAQ,CAA0B;gBAE9B,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,mBAAmB;IAOlD,OAAO,IAAI,OAAO,CAAC,aAAa,CAAC;IAgDvC,OAAO,CAAC,WAAW;IA+CnB,OAAO,CAAC,eAAe;CA2ExB"}

package/dist/compiler.js.map

@@ -1 +1 @@
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package/dist/engine.d.ts

@@ -5,34 +5,47 @@
  *   - Simple merge: concatenates files in order (v1)
  *   - Compile: resolves Handlebars templates + frontmatter tags (v2)
  */
-import { AgentConfig, BuildResult, ValidationResult } from './types';
+import { AgentConfig, ResolvedAgentConfig, RepoConfig, BuildResult, ValidationResult } from './types';
 export declare class InstruxEngine {
     private rootDir;
+    private repoConfig;
     constructor(rootDir?: string);
+    /**
+     * Load repository-level configuration from instrux.json at project root.
+     * This is cached after the first load.
+     */
+    loadRepoConfig(): Promise<RepoConfig | null>;
+    /**
+     * Merge repository config with agent config.
+     * Agent config takes precedence over repository config.
+     * Returns a config with all required fields populated.
+     */
+    private mergeConfigs;
     /**
      * Resolve the config path for a given agent name.
-     * Looks in `agents/<name>/agent.json`.
+     * Looks in `<agentsDir>/<name>/agent.json`.
      */
     private agentConfigPath;
     /**
      * Load an agent configuration by name.
+     * Merges with repository-level config if present.
      */
-    loadConfig(agentName: string): Promise<AgentConfig>;
+    loadConfig(agentName: string): Promise<ResolvedAgentConfig>;
     /**
-     * List all agents found in the `agents/` directory.
+     * List all agents found in the configured agents directory.
      */
     listAgents(): Promise<{
         name: string;
         config: AgentConfig | null;
     }[]>;
-    validate(config: AgentConfig): Promise<ValidationResult>;
-    merge(config: AgentConfig): Promise<string>;
-    writeOutput(config: AgentConfig, content: string): Promise<string>;
+    validate(config: ResolvedAgentConfig): Promise<ValidationResult>;
+    merge(config: ResolvedAgentConfig): Promise<string>;
+    writeOutput(config: ResolvedAgentConfig, content: string): Promise<string>;
     /**
      * Returns true if the agent config uses the template compiler (v2)
      * instead of simple ordered merge.
      */
-    isCompileMode(config: AgentConfig): boolean;
+    isCompileMode(config: ResolvedAgentConfig): boolean;
     build(agentName: string): Promise<BuildResult>;
     contentHash(content: string): string;
 }

package/dist/engine.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../src/engine.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH,OAAO,EACL,WAAW,EACX,WAAW,EACX,gBAAgB,EACjB,MAAM,SAAS,CAAC;AAGjB,qBAAa,aAAa;IACxB,OAAO,CAAC,OAAO,CAAS;gBAEZ,OAAO,CAAC,EAAE,MAAM;IAM5B;;;OAGG;IACH,OAAO,CAAC,eAAe;IAIvB;;OAEG;IACG,UAAU,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC;IAgBzD;;OAEG;IACG,UAAU,IAAI,OAAO,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,WAAW,GAAG,IAAI,CAAA;KAAE,EAAE,CAAC;IAgCrE,QAAQ,CAAC,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC;IAqBxD,KAAK,CAAC,MAAM,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC;IA+C3C,WAAW,CAAC,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IA4BxE;;;OAGG;IACH,aAAa,CAAC,MAAM,EAAE,WAAW,GAAG,OAAO;IAIrC,KAAK,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC;IAgDpD,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM;CAOrC"}
+{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../src/engine.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,UAAU,EACV,WAAW,EACX,gBAAgB,EAGjB,MAAM,SAAS,CAAC;AAGjB,qBAAa,aAAa;IACxB,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,UAAU,CAA2B;gBAEjC,OAAO,CAAC,EAAE,MAAM;IAM5B;;;OAGG;IACG,cAAc,IAAI,OAAO,CAAC,UAAU,GAAG,IAAI,CAAC;IAuBlD;;;;OAIG;IACH,OAAO,CAAC,YAAY;IAoBpB;;;OAGG;YACW,eAAe;IAM7B;;;OAGG;IACG,UAAU,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,mBAAmB,CAAC;IAoBjE;;OAEG;IACG,UAAU,IAAI,OAAO,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,WAAW,GAAG,IAAI,CAAA;KAAE,EAAE,CAAC;IAiCrE,QAAQ,CAAC,MAAM,EAAE,mBAAmB,GAAG,OAAO,CAAC,gBAAgB,CAAC;IAqBhE,KAAK,CAAC,MAAM,EAAE,mBAAmB,GAAG,OAAO,CAAC,MAAM,CAAC;IA+CnD,WAAW,CAAC,MAAM,EAAE,mBAAmB,EAAE,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IA4BhF;;;OAGG;IACH,aAAa,CAAC,MAAM,EAAE,mBAAmB,GAAG,OAAO;IAI7C,KAAK,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC;IAgDpD,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM;CAOrC"}

package/dist/engine.js

@@ -44,37 +44,92 @@ exports.InstruxEngine = void 0;
 const fs = __importStar(require("fs-extra"));
 const path = __importStar(require("path"));
 const crypto = __importStar(require("crypto"));
+const types_1 = require("./types");
 const compiler_1 = require("./compiler");
 class InstruxEngine {
     constructor(rootDir) {
+        this.repoConfig = null;
         this.rootDir = rootDir ?? process.cwd();
     }
+    // ── Repo config loading ───────────────────────
+    /**
+     * Load repository-level configuration from instrux.json at project root.
+     * This is cached after the first load.
+     */
+    async loadRepoConfig() {
+        if (this.repoConfig !== null) {
+            return this.repoConfig;
+        }
+        const configPath = path.join(this.rootDir, 'instrux.json');
+        if (!(await fs.pathExists(configPath))) {
+            this.repoConfig = {};
+            return this.repoConfig;
+        }
+        try {
+            const raw = await fs.readFile(configPath, 'utf-8');
+            this.repoConfig = JSON.parse(raw);
+            return this.repoConfig;
+        }
+        catch (err) {
+            console.warn(`⚠  Warning: Failed to parse instrux.json: ${err}`);
+            this.repoConfig = {};
+            return this.repoConfig;
+        }
+    }
+    /**
+     * Merge repository config with agent config.
+     * Agent config takes precedence over repository config.
+     * Returns a config with all required fields populated.
+     */
+    mergeConfigs(agentConfig, repoConfig) {
+        const mergeSettings = {
+            ...types_1.DEFAULT_MERGE_SETTINGS,
+            ...(repoConfig.mergeSettings ?? {}),
+            ...(agentConfig.mergeSettings ?? {}),
+        };
+        return {
+            ...agentConfig,
+            agentsDirectory: repoConfig.agentsDirectory ?? 'agents',
+            outputDirectory: agentConfig.outputDirectory ?? repoConfig.outputDirectory ?? 'out',
+            outputFilePattern: agentConfig.outputFilePattern ?? `${agentConfig.name.toLowerCase()}_instructions.md`,
+            sources: agentConfig.sources ?? repoConfig.sources,
+            frontmatter: agentConfig.frontmatter ?? repoConfig.frontmatter,
+            mergeSettings,
+        };
+    }
     // ── Config loading ───────────────────────────────────────
     /**
      * Resolve the config path for a given agent name.
-     * Looks in `agents/<name>/agent.json`.
+     * Looks in `<agentsDir>/<name>/agent.json`.
      */
-    agentConfigPath(agentName) {
-        return path.join(this.rootDir, 'agents', agentName, 'agent.json');
+    async agentConfigPath(agentName) {
+        const repoConfig = await this.loadRepoConfig();
+        const agentsDir = repoConfig?.agentsDirectory ?? 'agents';
+        return path.join(this.rootDir, agentsDir, agentName, 'agent.json');
     }
     /**
      * Load an agent configuration by name.
+     * Merges with repository-level config if present.
      */
     async loadConfig(agentName) {
-        const configPath = this.agentConfigPath(agentName);
+        const configPath = await this.agentConfigPath(agentName);
         if (!(await fs.pathExists(configPath))) {
             throw new Error(`Agent config not found: ${path.relative(this.rootDir, configPath)}\n` +
                 `Run "instrux init <name>" to create one.`);
         }
         const raw = await fs.readFile(configPath, 'utf-8');
-        return JSON.parse(raw);
+        const agentConfig = JSON.parse(raw);
+        // Load and merge repository config
+        const repoConfig = await this.loadRepoConfig();
+        return this.mergeConfigs(agentConfig, repoConfig ?? {});
     }
     // ── Discovery ────────────────────────────────────────────
     /**
-     * List all agents found in the `agents/` directory.
+     * List all agents found in the configured agents directory.
      */
     async listAgents() {
-        const agentsDir = path.join(this.rootDir, 'agents');
+        const repoConfig = await this.loadRepoConfig();
+        const agentsDir = path.join(this.rootDir, repoConfig?.agentsDirectory ?? 'agents');
         if (!(await fs.pathExists(agentsDir))) {
             return [];
         }