@ceyhunbilir/synaphex 1.0.1

package/README.md

@@ -0,0 +1,73 @@
+# Synaphex — Multi-Agent AI Pipeline for Code
+
+A **Claude Code skill** (plugin) that brings a 5-stage AI agent pipeline directly into your IDE:
+
+```
+Task
+  ↓
+[Examiner]       → Context Analysis
+  ↓
+[Researcher]     → Best Practices (optional in /fix mode)
+  ↓
+[Coder]          → Production-Ready Implementation
+  ↓
+[Questioner]     → Critical Review & Improvements
+  ↓
+[Reviewer]       → Final Quality Gate
+  ↓
+Output (Markdown + JSON)
+```
+
+Works across **Claude.ai**, **VS Code**, **JetBrains**, and any IDE running Claude Code.
+
+## Installation
+
+```bash
+npm install -g @ceyhunbilir/synaphex
+```
+
+This installs three Claude Code skills:
+- `/synaphex/init <project>` — Create a new project
+- `/synaphex/query <task>` — Full 5-stage pipeline
+- `/synaphex/fix <task>` — Quick fix (optional Researcher)
+
+## Quick Start
+
+### 1. Initialize a project
+
+```
+/synaphex/init my-project
+```
+
+Creates `~/.claude/projects/my-project/` with config, memory, and outputs.
+
+### 2. Run a full pipeline
+
+```
+/synaphex/query implement retry logic for HTTP requests
+```
+
+### 3. Run a quick fix
+
+```
+/synaphex/fix add null check to the API handler
+```
+
+Asks if you want to skip the research phase.
+
+## Project Structure
+
+```
+~/.claude/projects/<project>/
+├── config.md                  ← LLM provider & model
+├── memory/                    ← project context (preserved)
+└── outputs/                   ← pipeline results
+```
+
+## Configuration
+
+Edit `~/.claude/projects/<project>/config.md` to change LLM provider.
+
+## License
+
+MIT

package/dist/commands/init.d.ts

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+export declare function init(projectName: string): Promise<void>;
+//# sourceMappingURL=init.d.ts.map

package/dist/commands/init.d.ts.map

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+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AAEA,wBAAsB,IAAI,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAY7D"}

package/dist/commands/init.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.init = init;
+const project_1 = require("../lib/project");
+async function init(projectName) {
+    if (!projectName || !projectName.trim()) {
+        console.error('Error: project name is required');
+        process.exit(1);
+    }
+    try {
+        await (0, project_1.initializeProject)(projectName.trim());
+    }
+    catch (error) {
+        console.error('Error initializing project:', error instanceof Error ? error.message : error);
+        process.exit(1);
+    }
+}
+//# sourceMappingURL=init.js.map

package/dist/commands/init.js.map

@@ -0,0 +1 @@
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package/dist/commands/list-outputs.d.ts

@@ -0,0 +1,2 @@
+export declare function handleListOutputs(projectName: string): Promise<void>;
+//# sourceMappingURL=list-outputs.d.ts.map

package/dist/commands/list-outputs.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"list-outputs.d.ts","sourceRoot":"","sources":["../../src/commands/list-outputs.ts"],"names":[],"mappings":"AAEA,wBAAsB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAwB1E"}

package/dist/commands/list-outputs.js

@@ -0,0 +1,27 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handleListOutputs = handleListOutputs;
+const output_1 = require("../lib/output");
+async function handleListOutputs(projectName) {
+    if (!projectName || !projectName.trim()) {
+        console.error('Error: project name is required');
+        process.exit(1);
+    }
+    try {
+        const outputs = await (0, output_1.listOutputs)(projectName.trim());
+        if (outputs.length === 0) {
+            console.log('No pipeline outputs found.');
+            process.exit(0);
+        }
+        console.log(`Pipeline outputs for project "${projectName}":\n`);
+        outputs.forEach((output) => {
+            console.log(`  - ${output}`);
+        });
+        process.exit(0);
+    }
+    catch (error) {
+        console.error('Error listing outputs:', error instanceof Error ? error.message : error);
+        process.exit(1);
+    }
+}
+//# sourceMappingURL=list-outputs.js.map

package/dist/commands/list-outputs.js.map

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package/dist/commands/load-memory.d.ts

@@ -0,0 +1,2 @@
+export declare function handleLoadMemory(projectName: string): Promise<void>;
+//# sourceMappingURL=load-memory.d.ts.map

package/dist/commands/load-memory.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"load-memory.d.ts","sourceRoot":"","sources":["../../src/commands/load-memory.ts"],"names":[],"mappings":"AAEA,wBAAsB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAczE"}

package/dist/commands/load-memory.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handleLoadMemory = handleLoadMemory;
+const memory_1 = require("../lib/memory");
+async function handleLoadMemory(projectName) {
+    if (!projectName || !projectName.trim()) {
+        console.error('Error: project name is required');
+        process.exit(1);
+    }
+    try {
+        const memory = await (0, memory_1.loadMemory)(projectName.trim());
+        process.stdout.write(memory);
+        process.exit(0);
+    }
+    catch (error) {
+        console.error('Error loading memory:', error instanceof Error ? error.message : error);
+        process.exit(1);
+    }
+}
+//# sourceMappingURL=load-memory.js.map

package/dist/commands/load-memory.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"load-memory.js","sourceRoot":"","sources":["../../src/commands/load-memory.ts"],"names":[],"mappings":";;AAEA,4CAcC;AAhBD,0CAA2C;AAEpC,KAAK,UAAU,gBAAgB,CAAC,WAAmB;IACxD,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,CAAC,IAAI,EAAE,EAAE,CAAC;QACxC,OAAO,CAAC,KAAK,CAAC,iCAAiC,CAAC,CAAC;QACjD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,IAAA,mBAAU,EAAC,WAAW,CAAC,IAAI,EAAE,CAAC,CAAC;QACpD,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAC7B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,uBAAuB,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACvF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC"}

package/dist/commands/save-output.d.ts

@@ -0,0 +1,2 @@
+export declare function handleSaveOutput(projectName: string): Promise<void>;
+//# sourceMappingURL=save-output.d.ts.map

package/dist/commands/save-output.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"save-output.d.ts","sourceRoot":"","sources":["../../src/commands/save-output.ts"],"names":[],"mappings":"AAGA,wBAAsB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAiCzE"}

package/dist/commands/save-output.js

@@ -0,0 +1,37 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handleSaveOutput = handleSaveOutput;
+const output_1 = require("../lib/output");
+async function handleSaveOutput(projectName) {
+    if (!projectName || !projectName.trim()) {
+        console.error('Error: project name is required');
+        process.exit(1);
+    }
+    try {
+        // Read JSON from stdin
+        let jsonStr = '';
+        process.stdin.on('data', (chunk) => {
+            jsonStr += chunk.toString();
+        });
+        process.stdin.on('end', async () => {
+            try {
+                const output = JSON.parse(jsonStr);
+                await (0, output_1.saveOutput)(projectName.trim(), output);
+                process.exit(0);
+            }
+            catch (error) {
+                console.error('Error parsing JSON:', error instanceof Error ? error.message : error);
+                process.exit(1);
+            }
+        });
+        process.stdin.on('error', (error) => {
+            console.error('Error reading stdin:', error);
+            process.exit(1);
+        });
+    }
+    catch (error) {
+        console.error('Error:', error instanceof Error ? error.message : error);
+        process.exit(1);
+    }
+}
+//# sourceMappingURL=save-output.js.map

package/dist/commands/save-output.js.map

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+{"version":3,"file":"save-output.js","sourceRoot":"","sources":["../../src/commands/save-output.ts"],"names":[],"mappings":";;AAGA,4CAiCC;AApCD,0CAA2C;AAGpC,KAAK,UAAU,gBAAgB,CAAC,WAAmB;IACxD,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,CAAC,IAAI,EAAE,EAAE,CAAC;QACxC,OAAO,CAAC,KAAK,CAAC,iCAAiC,CAAC,CAAC;QACjD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,IAAI,CAAC;QACH,uBAAuB;QACvB,IAAI,OAAO,GAAG,EAAE,CAAC;QAEjB,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,KAAK,EAAE,EAAE;YACjC,OAAO,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;QAC9B,CAAC,CAAC,CAAC;QAEH,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,EAAE,KAAK,IAAI,EAAE;YACjC,IAAI,CAAC;gBACH,MAAM,MAAM,GAAmB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;gBACnD,MAAM,IAAA,mBAAU,EAAC,WAAW,CAAC,IAAI,EAAE,EAAE,MAAM,CAAC,CAAC;gBAC7C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,OAAO,CAAC,KAAK,CAAC,qBAAqB,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;gBACrF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;QACH,CAAC,CAAC,CAAC;QAEH,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,EAAE;YAClC,OAAO,CAAC,KAAK,CAAC,sBAAsB,EAAE,KAAK,CAAC,CAAC;YAC7C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC,CAAC,CAAC;IACL,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,QAAQ,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACxE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC"}

package/dist/index.d.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":""}

package/dist/index.js

@@ -0,0 +1,34 @@
+#!/usr/bin/env node
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const commander_1 = require("commander");
+const init_1 = require("./commands/init");
+const save_output_1 = require("./commands/save-output");
+const load_memory_1 = require("./commands/load-memory");
+const list_outputs_1 = require("./commands/list-outputs");
+const program = new commander_1.Command();
+program
+    .name('synaphex')
+    .description('Multi-agent AI pipeline for code analysis, generation, and improvement')
+    .version('1.0.0');
+program
+    .command('init-project <name>')
+    .description('Initialize a new Synaphex project at ~/.claude/projects/<name>')
+    .action(init_1.init);
+program
+    .command('save-output <project>')
+    .description('Save pipeline output (reads JSON from stdin)')
+    .action(save_output_1.handleSaveOutput);
+program
+    .command('load-memory <project>')
+    .description('Load and output project memory files')
+    .action(load_memory_1.handleLoadMemory);
+program
+    .command('list-outputs <project>')
+    .description('List all pipeline outputs for a project')
+    .action(list_outputs_1.handleListOutputs);
+program.parse(process.argv);
+if (!process.argv.slice(2).length) {
+    program.outputHelp();
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAEA,yCAAoC;AACpC,0CAAuC;AACvC,wDAA0D;AAC1D,wDAA0D;AAC1D,0DAA4D;AAE5D,MAAM,OAAO,GAAG,IAAI,mBAAO,EAAE,CAAC;AAE9B,OAAO;KACJ,IAAI,CAAC,UAAU,CAAC;KAChB,WAAW,CAAC,wEAAwE,CAAC;KACrF,OAAO,CAAC,OAAO,CAAC,CAAC;AAEpB,OAAO;KACJ,OAAO,CAAC,qBAAqB,CAAC;KAC9B,WAAW,CAAC,gEAAgE,CAAC;KAC7E,MAAM,CAAC,WAAI,CAAC,CAAC;AAEhB,OAAO;KACJ,OAAO,CAAC,uBAAuB,CAAC;KAChC,WAAW,CAAC,8CAA8C,CAAC;KAC3D,MAAM,CAAC,8BAAgB,CAAC,CAAC;AAE5B,OAAO;KACJ,OAAO,CAAC,uBAAuB,CAAC;KAChC,WAAW,CAAC,sCAAsC,CAAC;KACnD,MAAM,CAAC,8BAAgB,CAAC,CAAC;AAE5B,OAAO;KACJ,OAAO,CAAC,wBAAwB,CAAC;KACjC,WAAW,CAAC,yCAAyC,CAAC;KACtD,MAAM,CAAC,gCAAiB,CAAC,CAAC;AAE7B,OAAO,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;AAE5B,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;IAClC,OAAO,CAAC,UAAU,EAAE,CAAC;AACvB,CAAC"}

package/dist/lib/memory.d.ts

@@ -0,0 +1,3 @@
+export declare function loadMemory(projectName: string): Promise<string>;
+export declare function getMemoryIndex(projectName: string): Promise<string>;
+//# sourceMappingURL=memory.d.ts.map

package/dist/lib/memory.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"memory.d.ts","sourceRoot":"","sources":["../../src/lib/memory.ts"],"names":[],"mappings":"AAIA,wBAAsB,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CA0BrE;AAED,wBAAsB,cAAc,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAQzE"}

package/dist/lib/memory.js

@@ -0,0 +1,39 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.loadMemory = loadMemory;
+exports.getMemoryIndex = getMemoryIndex;
+const fs_extra_1 = __importDefault(require("fs-extra"));
+const path_1 = __importDefault(require("path"));
+const paths_1 = require("./paths");
+async function loadMemory(projectName) {
+    const memoryDir = paths_1.Paths.memory(projectName);
+    if (!await fs_extra_1.default.pathExists(memoryDir)) {
+        return '# No project memory found\n';
+    }
+    // Read all .md files in memory directory
+    const files = await fs_extra_1.default.readdir(memoryDir);
+    const mdFiles = files
+        .filter((f) => f.endsWith('.md') && f !== 'MEMORY.md')
+        .sort();
+    if (mdFiles.length === 0) {
+        return '# No memory entries found\n';
+    }
+    let combinedContent = '# Project Memory\n\n';
+    for (const file of mdFiles) {
+        const filePath = path_1.default.join(memoryDir, file);
+        const content = await fs_extra_1.default.readFile(filePath, 'utf-8');
+        combinedContent += `## ${file}\n\n${content}\n\n---\n\n`;
+    }
+    return combinedContent;
+}
+async function getMemoryIndex(projectName) {
+    const indexPath = paths_1.Paths.memoryIndex(projectName);
+    if (!await fs_extra_1.default.pathExists(indexPath)) {
+        return '# Memory Index Not Found\n';
+    }
+    return fs_extra_1.default.readFile(indexPath, 'utf-8');
+}
+//# sourceMappingURL=memory.js.map

package/dist/lib/memory.js.map

@@ -0,0 +1 @@
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package/dist/lib/output.d.ts

@@ -0,0 +1,4 @@
+import { PipelineOutput } from '../types';
+export declare function saveOutput(projectName: string, output: PipelineOutput): Promise<string>;
+export declare function listOutputs(projectName: string): Promise<string[]>;
+//# sourceMappingURL=output.d.ts.map

package/dist/lib/output.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"output.d.ts","sourceRoot":"","sources":["../../src/lib/output.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAC;AAmD1C,wBAAsB,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,MAAM,EAAE,cAAc,GAAG,OAAO,CAAC,MAAM,CAAC,CAmB7F;AAED,wBAAsB,WAAW,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAYxE"}

package/dist/lib/output.js

@@ -0,0 +1,77 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.saveOutput = saveOutput;
+exports.listOutputs = listOutputs;
+const fs_extra_1 = __importDefault(require("fs-extra"));
+const path_1 = __importDefault(require("path"));
+const crypto_1 = require("crypto");
+const paths_1 = require("./paths");
+function generateRunId() {
+    const now = new Date();
+    const timestamp = now
+        .toISOString()
+        .replace(/[-:]/g, '')
+        .replace(/\.\d{3}/, '');
+    const randomPart = (0, crypto_1.randomBytes)(4).toString('hex');
+    return `${timestamp.slice(0, 15)}_${randomPart}`;
+}
+function formatMarkdownOutput(output) {
+    const { command, task, skip_researcher, timestamp, stages } = output;
+    let markdown = `# Synaphex ${command.toUpperCase()} Pipeline Output
+
+**Run ID**: ${output.run_id}
+**Timestamp**: ${timestamp}
+**Task**: ${task}
+**Skip Researcher**: ${skip_researcher ? 'Yes' : 'No'}
+
+---
+
+`;
+    if (stages.examiner) {
+        markdown += `## Stage 1: Examiner\n\n${stages.examiner}\n\n---\n\n`;
+    }
+    if (stages.researcher && !skip_researcher) {
+        markdown += `## Stage 2: Researcher\n\n${stages.researcher}\n\n---\n\n`;
+    }
+    if (stages.coder) {
+        markdown += `## Stage ${skip_researcher ? '2' : '3'}: Coder\n\n${stages.coder}\n\n---\n\n`;
+    }
+    if (stages.questioner) {
+        markdown += `## Stage ${skip_researcher ? '3' : '4'}: Questioner\n\n${stages.questioner}\n\n---\n\n`;
+    }
+    if (stages.reviewer) {
+        markdown += `## Stage ${skip_researcher ? '4' : '5'}: Reviewer\n\n${stages.reviewer}\n\n---\n\n`;
+    }
+    markdown += `Generated by Synaphex on ${new Date().toLocaleString()}`;
+    return markdown;
+}
+async function saveOutput(projectName, output) {
+    const outputsDir = paths_1.Paths.outputs(projectName);
+    await fs_extra_1.default.ensureDir(outputsDir);
+    const runId = generateRunId();
+    const outputWithId = { ...output, run_id: runId };
+    // Save JSON
+    const jsonPath = path_1.default.join(outputsDir, `run_${runId}.json`);
+    await fs_extra_1.default.writeJSON(jsonPath, outputWithId, { spaces: 2 });
+    // Save Markdown
+    const mdContent = formatMarkdownOutput(outputWithId);
+    const mdPath = path_1.default.join(outputsDir, `run_${runId}.md`);
+    await fs_extra_1.default.writeFile(mdPath, mdContent, 'utf-8');
+    console.log(`✓ Output saved: ${jsonPath}`);
+    return runId;
+}
+async function listOutputs(projectName) {
+    const outputsDir = paths_1.Paths.outputs(projectName);
+    if (!await fs_extra_1.default.pathExists(outputsDir)) {
+        return [];
+    }
+    const files = await fs_extra_1.default.readdir(outputsDir);
+    return files
+        .filter((f) => f.endsWith('.json'))
+        .sort()
+        .reverse();
+}
+//# sourceMappingURL=output.js.map

package/dist/lib/output.js.map

@@ -0,0 +1 @@
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package/dist/lib/paths.d.ts

@@ -0,0 +1,11 @@
+export declare const Paths: {
+    claudeHome: string;
+    commandsDir: string;
+    projectsDir: string;
+    project: (name: string) => string;
+    memory: (name: string) => string;
+    memoryIndex: (name: string) => string;
+    config: (name: string) => string;
+    outputs: (name: string) => string;
+};
+//# sourceMappingURL=paths.d.ts.map

package/dist/lib/paths.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"paths.d.ts","sourceRoot":"","sources":["../../src/lib/paths.ts"],"names":[],"mappings":"AAMA,eAAO,MAAM,KAAK;;;;oBAKA,MAAM,KAAG,MAAM;mBAChB,MAAM,KAAG,MAAM;wBACV,MAAM,KAAG,MAAM;mBACpB,MAAM,KAAG,MAAM;oBACd,MAAM,KAAG,MAAM;CAChC,CAAC"}

package/dist/lib/paths.js

@@ -0,0 +1,21 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Paths = void 0;
+const os_1 = __importDefault(require("os"));
+const path_1 = __importDefault(require("path"));
+const CLAUDE_HOME = path_1.default.join(os_1.default.homedir(), '.claude');
+const PROJECTS_DIR = path_1.default.join(CLAUDE_HOME, 'projects');
+exports.Paths = {
+    claudeHome: CLAUDE_HOME,
+    commandsDir: path_1.default.join(CLAUDE_HOME, 'commands', 'synaphex'),
+    projectsDir: PROJECTS_DIR,
+    project: (name) => path_1.default.join(PROJECTS_DIR, name),
+    memory: (name) => path_1.default.join(PROJECTS_DIR, name, 'memory'),
+    memoryIndex: (name) => path_1.default.join(PROJECTS_DIR, name, 'memory', 'MEMORY.md'),
+    config: (name) => path_1.default.join(PROJECTS_DIR, name, 'config.md'),
+    outputs: (name) => path_1.default.join(PROJECTS_DIR, name, 'outputs'),
+};
+//# sourceMappingURL=paths.js.map

package/dist/lib/paths.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"paths.js","sourceRoot":"","sources":["../../src/lib/paths.ts"],"names":[],"mappings":";;;;;;AAAA,4CAAoB;AACpB,gDAAwB;AAExB,MAAM,WAAW,GAAG,cAAI,CAAC,IAAI,CAAC,YAAE,CAAC,OAAO,EAAE,EAAE,SAAS,CAAC,CAAC;AACvD,MAAM,YAAY,GAAG,cAAI,CAAC,IAAI,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC;AAE3C,QAAA,KAAK,GAAG;IACnB,UAAU,EAAE,WAAW;IACvB,WAAW,EAAE,cAAI,CAAC,IAAI,CAAC,WAAW,EAAE,UAAU,EAAE,UAAU,CAAC;IAC3D,WAAW,EAAE,YAAY;IAEzB,OAAO,EAAE,CAAC,IAAY,EAAU,EAAE,CAAC,cAAI,CAAC,IAAI,CAAC,YAAY,EAAE,IAAI,CAAC;IAChE,MAAM,EAAE,CAAC,IAAY,EAAU,EAAE,CAAC,cAAI,CAAC,IAAI,CAAC,YAAY,EAAE,IAAI,EAAE,QAAQ,CAAC;IACzE,WAAW,EAAE,CAAC,IAAY,EAAU,EAAE,CAAC,cAAI,CAAC,IAAI,CAAC,YAAY,EAAE,IAAI,EAAE,QAAQ,EAAE,WAAW,CAAC;IAC3F,MAAM,EAAE,CAAC,IAAY,EAAU,EAAE,CAAC,cAAI,CAAC,IAAI,CAAC,YAAY,EAAE,IAAI,EAAE,WAAW,CAAC;IAC5E,OAAO,EAAE,CAAC,IAAY,EAAU,EAAE,CAAC,cAAI,CAAC,IAAI,CAAC,YAAY,EAAE,IAAI,EAAE,SAAS,CAAC;CAC5E,CAAC"}

package/dist/lib/project.d.ts

@@ -0,0 +1,2 @@
+export declare function initializeProject(projectName: string): Promise<void>;
+//# sourceMappingURL=project.d.ts.map

package/dist/lib/project.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"project.d.ts","sourceRoot":"","sources":["../../src/lib/project.ts"],"names":[],"mappings":"AAIA,wBAAsB,iBAAiB,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA2E1E"}

package/dist/lib/project.js

@@ -0,0 +1,78 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.initializeProject = initializeProject;
+const fs_extra_1 = __importDefault(require("fs-extra"));
+const path_1 = __importDefault(require("path"));
+const paths_1 = require("./paths");
+async function initializeProject(projectName) {
+    const projectPath = paths_1.Paths.project(projectName);
+    const memoryPath = paths_1.Paths.memory(projectName);
+    const outputsPath = paths_1.Paths.outputs(projectName);
+    const configPath = paths_1.Paths.config(projectName);
+    const memoryIndexPath = paths_1.Paths.memoryIndex(projectName);
+    // Create directories
+    await fs_extra_1.default.ensureDir(memoryPath);
+    await fs_extra_1.default.ensureDir(outputsPath);
+    // Create config.md with YAML front-matter
+    const now = new Date().toISOString();
+    const configContent = `---
+project: ${projectName}
+provider: claude
+model: claude-opus-4-5
+created_at: ${now}
+---
+
+# Project Configuration
+
+Edit this file to change the LLM provider and model for this project.
+
+## Supported Providers
+
+- **claude** — Anthropic Claude (requires ANTHROPIC_API_KEY)
+- **openai** — OpenAI-compatible including Copilot (requires OPENAI_API_KEY)
+- **gemini** — Google Gemini (requires GEMINI_API_KEY)
+
+## Current Settings
+
+Provider: claude
+Model: claude-opus-4-5
+Created: ${now}
+`;
+    await fs_extra_1.default.writeFile(configPath, configContent, 'utf-8');
+    // Create memory/MEMORY.md index
+    const memoryIndexContent = `# Project Memory Index: ${projectName}
+
+Add memory entries below as the project evolves.
+
+## Entries
+
+- [Overview](overview.md) — project overview and context
+`;
+    await fs_extra_1.default.writeFile(memoryIndexPath, memoryIndexContent, 'utf-8');
+    // Create memory/overview.md
+    const overviewContent = `---
+name: Project Overview
+description: Initial project overview
+type: project
+---
+
+# ${projectName}
+
+Project initialized at ${now}.
+
+## Quick Links
+
+- **Config**: ../config.md
+- **Outputs**: ../outputs/ (pipeline run results)
+`;
+    const overviewPath = path_1.default.join(memoryPath, 'overview.md');
+    await fs_extra_1.default.writeFile(overviewPath, overviewContent, 'utf-8');
+    console.log(`✓ Project initialized: ${projectPath}`);
+    console.log(`  - Config: ${configPath}`);
+    console.log(`  - Memory: ${memoryPath}`);
+    console.log(`  - Outputs: ${outputsPath}`);
+}
+//# sourceMappingURL=project.js.map

package/dist/lib/project.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"project.js","sourceRoot":"","sources":["../../src/lib/project.ts"],"names":[],"mappings":";;;;;AAIA,8CA2EC;AA/ED,wDAA0B;AAC1B,gDAAwB;AACxB,mCAAgC;AAEzB,KAAK,UAAU,iBAAiB,CAAC,WAAmB;IACzD,MAAM,WAAW,GAAG,aAAK,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC;IAC/C,MAAM,UAAU,GAAG,aAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;IAC7C,MAAM,WAAW,GAAG,aAAK,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC;IAC/C,MAAM,UAAU,GAAG,aAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;IAC7C,MAAM,eAAe,GAAG,aAAK,CAAC,WAAW,CAAC,WAAW,CAAC,CAAC;IAEvD,qBAAqB;IACrB,MAAM,kBAAE,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC;IAC/B,MAAM,kBAAE,CAAC,SAAS,CAAC,WAAW,CAAC,CAAC;IAEhC,0CAA0C;IAC1C,MAAM,GAAG,GAAG,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IACrC,MAAM,aAAa,GAAG;WACb,WAAW;;;cAGR,GAAG;;;;;;;;;;;;;;;;;WAiBN,GAAG;CACb,CAAC;IAEA,MAAM,kBAAE,CAAC,SAAS,CAAC,UAAU,EAAE,aAAa,EAAE,OAAO,CAAC,CAAC;IAEvD,gCAAgC;IAChC,MAAM,kBAAkB,GAAG,2BAA2B,WAAW;;;;;;;CAOlE,CAAC;IAEA,MAAM,kBAAE,CAAC,SAAS,CAAC,eAAe,EAAE,kBAAkB,EAAE,OAAO,CAAC,CAAC;IAEjE,4BAA4B;IAC5B,MAAM,eAAe,GAAG;;;;;;IAMtB,WAAW;;yBAEU,GAAG;;;;;;CAM3B,CAAC;IAEA,MAAM,YAAY,GAAG,cAAI,CAAC,IAAI,CAAC,UAAU,EAAE,aAAa,CAAC,CAAC;IAC1D,MAAM,kBAAE,CAAC,SAAS,CAAC,YAAY,EAAE,eAAe,EAAE,OAAO,CAAC,CAAC;IAE3D,OAAO,CAAC,GAAG,CAAC,0BAA0B,WAAW,EAAE,CAAC,CAAC;IACrD,OAAO,CAAC,GAAG,CAAC,eAAe,UAAU,EAAE,CAAC,CAAC;IACzC,OAAO,CAAC,GAAG,CAAC,eAAe,UAAU,EAAE,CAAC,CAAC;IACzC,OAAO,CAAC,GAAG,CAAC,gBAAgB,WAAW,EAAE,CAAC,CAAC;AAC7C,CAAC"}

package/dist/types.d.ts

@@ -0,0 +1,31 @@
+export interface ProjectConfig {
+    project: string;
+    provider: 'claude' | 'openai' | 'gemini';
+    model: string;
+    created_at: string;
+}
+export interface PipelineStages {
+    examiner?: string;
+    researcher?: string;
+    coder?: string;
+    questioner?: string;
+    reviewer?: string;
+}
+export interface PipelineOutput {
+    run_id: string;
+    command: 'query' | 'fix';
+    task: string;
+    skip_researcher: boolean;
+    timestamp: string;
+    stages: PipelineStages;
+}
+export interface MemoryEntry {
+    title: string;
+    file: string;
+    summary: string;
+}
+export interface MemoryIndex {
+    project: string;
+    entries: MemoryEntry[];
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,aAAa;IAC5B,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,QAAQ,GAAG,QAAQ,GAAG,QAAQ,CAAC;IACzC,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,OAAO,GAAG,KAAK,CAAC;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,eAAe,EAAE,OAAO,CAAC;IACzB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,cAAc,CAAC;CACxB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,WAAW;IAC1B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,WAAW,EAAE,CAAC;CACxB"}

package/dist/types.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=types.js.map

package/dist/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":""}

package/package.json

@@ -0,0 +1,50 @@
+{
+  "name": "@ceyhunbilir/synaphex",
+  "version": "1.0.1",
+  "description": "Multi-agent AI pipeline as a Claude Code skill — Examiner → Researcher → Coder → Questioner → Reviewer",
+  "main": "dist/index.js",
+  "bin": {
+    "synaphex": "dist/index.js"
+  },
+  "scripts": {
+    "build": "tsc",
+    "postinstall": "node scripts/postinstall.js",
+    "prepublishOnly": "npm run build",
+    "prepare": "husky install 2>/dev/null || true",
+    "lint:commit": "commitlint --from HEAD~1 --to HEAD"
+  },
+  "files": [
+    "dist/",
+    "skills/",
+    "scripts/postinstall.js"
+  ],
+  "keywords": [
+    "claude-code",
+    "ai-pipeline",
+    "multi-agent",
+    "skill",
+    "claude"
+  ],
+  "author": "ceyhunbilir",
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/ceyhunbilir/synaphex.git"
+  },
+  "homepage": "https://github.com/ceyhunbilir/synaphex",
+  "dependencies": {
+    "commander": "^12.0.0",
+    "fs-extra": "^11.2.0"
+  },
+  "devDependencies": {
+    "@commitlint/cli": "^18.0.0",
+    "@commitlint/config-conventional": "^18.0.0",
+    "@types/fs-extra": "^11.0.4",
+    "@types/node": "^20.0.0",
+    "husky": "^8.0.0",
+    "typescript": "^5.4.0"
+  },
+  "engines": {
+    "node": ">=18.0.0"
+  }
+}

package/scripts/postinstall.js

@@ -0,0 +1,43 @@
+#!/usr/bin/env node
+'use strict';
+
+const fs = require('fs');
+const path = require('path');
+const os = require('os');
+
+const SKILLS_SRC = path.join(__dirname, '..', 'skills');
+const COMMANDS_DEST = path.join(os.homedir(), '.claude', 'commands', 'synaphex');
+
+try {
+  // Create destination directory
+  fs.mkdirSync(COMMANDS_DEST, { recursive: true });
+
+  // Find all .md files in skills directory
+  const files = fs.readdirSync(SKILLS_SRC).filter((f) => f.endsWith('.md'));
+
+  if (files.length === 0) {
+    console.warn('[synaphex] Warning: No skill files found in skills/ directory');
+    process.exit(0);
+  }
+
+  // Copy each skill file
+  for (const file of files) {
+    const src = path.join(SKILLS_SRC, file);
+    const dest = path.join(COMMANDS_DEST, file);
+    fs.copyFileSync(src, dest);
+    console.log(`[synaphex] ✓ Installed skill: ~/.claude/commands/synaphex/${file}`);
+  }
+
+  console.log('\n[synaphex] Skills installed successfully!');
+  console.log('[synaphex] Available commands:');
+  console.log('  /synaphex/init <project>');
+  console.log('  /synaphex/query <task>');
+  console.log('  /synaphex/fix <task>');
+  console.log('\n[synaphex] Documentation: https://github.com/ceyhunbilir/synaphex');
+} catch (err) {
+  // Non-fatal error — postinstall script failures block npm install
+  console.warn('[synaphex] ⚠️  Warning: Could not auto-install skills:', err.message);
+  console.warn('[synaphex] You can manually copy them:');
+  console.warn(`  cp ${SKILLS_SRC}/*.md ~/.claude/commands/synaphex/`);
+  process.exit(0);
+}

package/skills/fix.md

@@ -0,0 +1,188 @@
+---
+description: "Run Synaphex fix pipeline with optional researcher skip: Examiner → [Researcher?] → Coder → Questioner → Reviewer"
+---
+
+# Synaphex Fix Pipeline
+
+**Fix Request:** $ARGUMENTS
+
+You are running the Synaphex fix pipeline. This is tailored for targeted bug fixes or code improvements where you may not need extensive research.
+
+---
+
+## Step 1: Ask About Research Phase
+
+Before starting, I need your input on whether to include the Researcher stage:
+
+> **Would you like to include the Researcher phase?**
+>
+> - **Yes** — Full pipeline (Examiner → Researcher → Coder → Questioner → Reviewer)
+>   - More thorough, researches best practices and solutions
+>   - Takes longer
+>   - Good for complex fixes or unclear requirements
+>
+> - **No** — Fast pipeline (Examiner → Coder → Questioner → Reviewer)
+>   - Skips research, goes straight to implementation
+>   - Faster, assumes you know what to do
+>   - Good for straightforward fixes or when you're confident in the approach
+
+Please respond with **Yes** or **No**.
+
+---
+
+## Pipeline Execution (Based on Your Choice)
+
+Based on your response above, I'll now run the appropriate pipeline.
+
+### Stage 1: EXAMINER — Context Analysis
+
+**Role:** Project context analyst. Understand what needs to be fixed.
+
+**Your Instructions:**
+
+1. **Analyze the fix request.** What exactly needs to be fixed or improved?
+
+2. **Examine the relevant code.** Read and understand:
+   - The code that needs fixing
+   - Related code that might be affected
+   - Existing patterns and conventions
+
+3. **Load project memory** (if available):
+   ```bash
+   synaphex load-memory $ARGUMENTS
+   ```
+
+4. **Identify the problem** and its context.
+
+**Produce:** Context report with sections:
+- **Problem Statement** — What's broken or needs improvement
+- **Root Cause Analysis** — Why is it happening?
+- **Affected Code** — Files and functions involved
+- **Current Patterns** — How similar issues are handled
+- **Impact Assessment** — What breaks if not fixed?
+- **Fix Strategy Outline** — Initial approach
+
+---
+
+### Stage 2 (OPTIONAL): RESEARCHER — Best Practices
+
+**⚠️ SKIP THIS STAGE IF USER CHOSE "NO"**
+
+**Role:** Research analyst. Find the best approach to fix this.
+
+**Your Instructions:**
+
+1. **Research the problem domain.**
+   - What are standard solutions for this type of issue?
+   - Are there libraries or patterns that help?
+
+2. **Evaluate fix approaches.**
+   - What are the options?
+   - What are trade-offs?
+   - What's most maintainable?
+
+3. **Document best practices** for this type of fix.
+
+**Produce:** Research report with sections:
+- **Recommended Fix** — Detailed approach
+- **Why This Approach** — Rationale
+- **Best Practices** — How to do this right
+- **Potential Issues** — What to watch out for
+- **Reference Examples** — Similar patterns in codebase
+
+---
+
+### Stage 3: CODER — Implementation
+
+**Role:** Senior developer. Write the fix.
+
+**Your Instructions:**
+
+1. **Implement the fix.** Based on Examiner (and Researcher if included):
+   - Write clean, tested code
+   - Follow existing patterns
+   - Include error handling
+   - Add comments where needed
+
+2. **Keep it focused.** This is a fix, not a refactor.
+   - Don't change unrelated code
+   - Don't add features beyond the fix
+   - Minimal necessary changes
+
+3. **Provide complete code** for all files that need changes.
+
+**Produce:** Implementation with sections:
+- **Code Changes** — Exact changes needed
+- **Why This Fixes It** — Explanation of the fix
+- **Side Effects** — Any other code that might be affected
+- **Testing** — How to verify the fix works
+
+---
+
+### Stage 4: QUESTIONER — Critical Review
+
+**Role:** Critical reviewer. Challenge the fix.
+
+**Your Instructions:**
+
+1. **Question the implementation.**
+   - Does it fully fix the issue?
+   - Are there edge cases?
+   - Could it break something else?
+   - Is error handling sufficient?
+
+2. **Identify improvements** and issues.
+
+3. **Suggest concrete fixes** with code examples.
+
+**Produce:** Critique with sections:
+- **Does It Fix The Problem?** — Yes/no assessment
+- **Edge Cases** — Scenarios not covered
+- **Potential Issues** — Bugs or problems the fix could introduce
+- **Improvements** — Better approaches
+- **Revised Code** — Specific fixes for issues found
+
+---
+
+### Stage 5: REVIEWER — Final Decision
+
+**Role:** Senior architect. Final quality gate.
+
+**Your Instructions:**
+
+1. **Review all prior outputs.**
+   - Is the fix correct?
+   - Is it complete?
+   - Are all Questioner feedback incorporated?
+
+2. **Make final decision:** APPROVED or NEEDS REVISION
+
+3. **Deliver the final implementation.**
+
+**Produce:** Final assessment with sections:
+- **Final Verdict** — APPROVED or NEEDS REVISION
+- **Complete Implementation** — Final fixed code
+- **Quality Verification** — Checklist of concerns addressed
+- **Impact Summary** — What changed and why
+- **Next Steps** (if any)
+
+---
+
+## Save Pipeline Output
+
+After all stages complete:
+
+```bash
+synaphex save-output $ARGUMENTS '{"command":"fix","task":"$ARGUMENTS","skip_researcher":false,"timestamp":"$(date -u +%Y-%m-%dT%H:%M:%SZ)","stages":{"examiner":"...","coder":"...","questioner":"...","reviewer":"..."}}'
+```
+
+(Set `skip_researcher` to `true` if the user chose to skip the research phase.)
+
+---
+
+## Important Notes
+
+- **Focused fixes:** This is for targeted fixes, not full rewrites
+- **Hard failure guards:** Stop immediately if any stage fails
+- **Quick feedback loops:** Fix pipeline is faster than query because research is optional
+- **Researcher inclusion:** Is your choice — skip for confidence, include for thorough vetting

package/skills/init.md

@@ -0,0 +1,50 @@
+---
+description: "Initialize a new Synaphex project at ~/.claude/projects/<project> with config, memory, and outputs directories"
+---
+
+# Synaphex Init
+
+I'll initialize a new Synaphex project for you. The project name is: **$ARGUMENTS**
+
+## Step 1: Create Project Directory
+
+Let me create the project structure:
+
+```bash
+synaphex init-project $ARGUMENTS
+```
+
+This creates `~/.claude/projects/$ARGUMENTS/` with:
+- **config.md** — LLM provider and model settings
+- **memory/** — project memory files for context across sessions
+- **outputs/** — pipeline run results
+
+## Step 2: Configure LLM Provider
+
+Your project is initialized with **Claude (Anthropic)** as the default provider.
+
+The available providers are:
+
+1. **claude** — Anthropic Claude (requires `ANTHROPIC_API_KEY`)
+   - Recommended: `claude-opus-4-5`
+   
+2. **openai** — OpenAI API compatible (includes Copilot, GPT-4)
+   - Requires: `OPENAI_API_KEY`
+   - Recommended: `gpt-4-turbo`
+   
+3. **gemini** — Google Gemini
+   - Requires: `GEMINI_API_KEY`
+   - Recommended: `gemini-pro`
+
+Would you like to keep Claude as your provider, or would you prefer to use OpenAI or Gemini?
+
+If you want to change it, I can update the config file for you.
+
+## Step 3: Ready to Go
+
+Your project **$ARGUMENTS** is ready! You can now use:
+
+- **`/synaphex/query <task>`** — Run the full 5-stage pipeline
+- **`/synaphex/fix <task>`** — Run the pipeline with optional Researcher skip
+
+Each pipeline run will be saved to `~/.claude/projects/$ARGUMENTS/outputs/` automatically.

package/skills/query.md

@@ -0,0 +1,193 @@
+---
+description: "Run the full Synaphex 5-stage pipeline: Examiner → Researcher → Coder → Questioner → Reviewer"
+---
+
+# Synaphex Query Pipeline
+
+**Task:** $ARGUMENTS
+
+You are running the complete Synaphex multi-agent pipeline. This will take you through 5 stages of analysis and refinement. Think deeply at each stage and produce thorough, high-quality outputs.
+
+---
+
+## Stage 1: EXAMINER — Context Analysis
+
+**Role:** You are a project context analyst. Your job is to understand the current state and what needs to be done.
+
+**Your Instructions:**
+
+1. **Analyze the task.** What exactly is being asked? What are the success criteria?
+
+2. **Examine the current codebase.** Read relevant files to understand:
+   - Existing architecture and patterns
+   - Technology stack in use
+   - File structure and organization
+   - Existing implementations that are related
+
+3. **Identify constraints and context.**
+   - What patterns are already established?
+   - What libraries/frameworks are in use?
+   - What conventions should be followed?
+
+4. **Load project memory** (if available). Run:
+   ```bash
+   synaphex load-memory $ARGUMENTS
+   ```
+   Review the output to understand project history and context.
+
+**Produce:** A comprehensive context report with sections:
+- **Task Analysis** — What needs to be done and why
+- **Current State** — Existing code, architecture, patterns
+- **Technology Stack** — Languages, frameworks, libraries in use
+- **Constraints & Conventions** — What to follow
+- **Identified Gaps** — What's missing or needs improvement
+- **Recommended Approach** — Initial strategy
+
+---
+
+## Stage 2: RESEARCHER — Best Practices & Solutions
+
+**Role:** You are a research analyst. Based on the context from Examiner, research the best approach.
+
+**Your Instructions:**
+
+1. **Research the problem domain.** What are the accepted best practices for this type of task?
+
+2. **Evaluate approaches.** Consider:
+   - Multiple solutions and their trade-offs
+   - Performance implications
+   - Security considerations
+   - Maintainability and readability
+   - Testing strategies
+
+3. **Check for existing solutions.** Are there libraries, patterns, or examples that directly apply?
+
+4. **Document findings.** Be specific about why certain approaches are better.
+
+**Produce:** A structured research report with sections:
+- **Recommended Approach** — Detailed explanation and rationale
+- **Alternative Approaches** — What else could work (and why you rejected them)
+- **Best Practices** — Security, performance, testing, patterns
+- **Relevant Libraries/Tools** — What to use and why
+- **Common Pitfalls** — What to avoid
+- **Reference Implementation** — Code examples or patterns to follow
+
+---
+
+## Stage 3: CODER — Implementation
+
+**Role:** You are a senior developer. Implement the solution based on all prior analysis.
+
+**Your Instructions:**
+
+1. **Write production-ready code.** This means:
+   - Follow the patterns identified by the Examiner
+   - Use the approaches recommended by the Researcher
+   - Include proper error handling
+   - Write clear, maintainable code
+   - Add comments for non-obvious logic
+   - Include type hints/types where applicable
+
+2. **Comprehensive implementation.** Provide:
+   - All necessary file changes or new files
+   - Complete, runnable code (not pseudocode)
+   - Integration points with existing code
+   - Usage examples or tests
+
+3. **Quality standards:**
+   - Consistent with the existing codebase style
+   - No unnecessary complexity
+   - Proper structure and organization
+   - Security-conscious (validate inputs, prevent common attacks)
+
+**Produce:** Complete implementation with sections:
+- **Code Changes** — All files to create or modify
+- **Key Implementation Details** — How it works, important decisions
+- **Integration Points** — Where this connects to existing code
+- **Usage Examples** — How to use the new code
+- **Testing Suggestions** — How to verify it works
+
+---
+
+## Stage 4: QUESTIONER — Critical Review
+
+**Role:** You are a critical code reviewer (Socratic method). Challenge every assumption.
+
+**Your Instructions:**
+
+1. **Question the implementation.**
+   - Does it handle all edge cases?
+   - Are there security vulnerabilities?
+   - Could it be more performant?
+   - Is the error handling sufficient?
+
+2. **Identify improvements:**
+   - Critical issues (must fix)
+   - Optimization opportunities
+   - Better patterns or libraries
+   - Edge cases not handled
+
+3. **Suggest concrete fixes.** For each issue, provide:
+   - What's wrong
+   - Why it matters
+   - Specific fix with code examples
+
+**Produce:** A structured critique with sections:
+- **Strengths** — What the implementation does well
+- **Critical Issues** — Things that must be fixed
+- **Suggested Improvements** — Better approaches, edge cases
+- **Performance Considerations** — Any bottlenecks?
+- **Security Review** — Any vulnerabilities?
+- **Revised Code Snippets** — Specific fixes for the most important issues
+
+---
+
+## Stage 5: REVIEWER — Final Quality Gate
+
+**Role:** You are a senior architect doing final review. Consolidate everything and deliver the final solution.
+
+**Your Instructions:**
+
+1. **Review all prior outputs holistically.**
+   - Does the final code address the original task?
+   - Have all Questioner feedback been incorporated?
+   - Is the solution complete and coherent?
+
+2. **Make a final decision:** APPROVED or NEEDS REVISION
+
+3. **If APPROVED:**
+   - Provide the complete, final implementation incorporating all improvements
+   - Explain what changed from Coder → final version
+   - Summarize the quality gates passed
+
+4. **If NEEDS REVISION:**
+   - Identify what's blocking approval
+   - Provide specific next steps
+
+**Produce:** Final verdict with sections:
+- **Final Verdict** — APPROVED or NEEDS REVISION (and why)
+- **Complete Implementation** — The final, polished code
+- **Changes Made** — Summary of improvements from Questioner feedback
+- **Quality Summary** — Verification checklist
+- **Next Steps** (if applicable) — What remains to be done
+
+---
+
+## Save Pipeline Output
+
+After all 5 stages complete successfully, save the results:
+
+```bash
+synaphex save-output <project-name> '{"command":"query","task":"$ARGUMENTS","skip_researcher":false,"timestamp":"$(date -u +%Y-%m-%dT%H:%M:%SZ)","stages":{"examiner":"...","researcher":"...","coder":"...","questioner":"...","reviewer":"..."}}'
+```
+
+(Note: In practice, this would be a complete JSON object with all stage outputs. You can output this to a file and pipe it to the save command if the output is large.)
+
+---
+
+## Important Notes
+
+- **Hard failure guards:** If any prior stage fails or produces no output, immediately stop the pipeline and report the failure. Do not continue.
+- **Token budget awareness:** Coder stage gets the most tokens (produces the most detailed code). Reviewer stage is concise.
+- **Output format:** Each stage should have clear section headers and complete thoughts.
+- **Quality over speed:** Take time to do this right. Better to produce a thorough output than a rushed one.