@jokerized/getresearchdone 0.4.1

package/commands/wireup.md

@@ -0,0 +1,29 @@
+---
+description: Discover unwired features and test integration wiring end-to-end
+argument-hint: "[--target <feature>] [--dry-run]"
+---
+
+Run the wireup command to discover integration gaps and validate feature wiring end-to-end:
+
+```bash
+node ${CLAUDE_PLUGIN_ROOT}/bin/grd-tools.js wireup run $ARGUMENTS
+```
+
+The wireup loop uses a pipeline architecture per iteration:
+1. Discovers features that exist in the codebase but lack full integration (exported-but-uncalled, config-without-surface, endpoint-without-integration-test)
+2. Generates executable test scenarios for each unwired feature (HTTP, CLI, and assert steps)
+3. Executes HTTP and CLI scenarios against the running system
+4. Detects missing connections from failed scenario results
+5. Reports a pass/fail summary with issue counts and recommended fixes
+
+Flags:
+- `--target <feature>` — Focus wireup on a specific feature area (filters discovered features by name match)
+- `--dry-run` — Discover and generate scenarios without executing them (useful for previewing what would run)
+- `--timeout N` — Timeout per subprocess in minutes
+- `--max-turns N` — Max turns per subprocess
+
+All operations enforce a sonnet model ceiling — no opus-class models are used.
+
+IMPORTANT: This command is long-running (spawns Claude subprocesses for scenario execution). You MUST run it in the background using `run_in_background: true` on the Bash tool to avoid hitting the Bash tool's default timeout. Use `TaskOutput` with `block: false` to check progress periodically.
+
+Report the JSON results. If any scenarios failed, explain what the missing connections are and suggest remediation steps.

package/dist/bin/gd.d.ts

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

package/dist/bin/gd.d.ts.map

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

package/dist/bin/gd.js

@@ -0,0 +1,178 @@
+#!/usr/bin/env node
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+const { join } = require('path');
+const { readFileSync, existsSync } = require('fs');
+const { parseFlags, classifyCommand, } = require('../lib/cli/index');
+const { runToolCommand, } = require('../lib/cli/tools');
+const { runAgentCommand, } = require('../lib/cli/agent');
+const flags = parseFlags(process.argv.slice(2));
+// --version
+if (flags.version) {
+    try {
+        // Handle both bin/ (source) and dist/bin/ (compiled) locations
+        let pkgPath = join(__dirname, '..', 'package.json');
+        if (!existsSync(pkgPath))
+            pkgPath = join(__dirname, '..', '..', 'package.json');
+        const pkg = JSON.parse(readFileSync(pkgPath, 'utf-8'));
+        process.stdout.write(`gd v${pkg.version}\n`);
+    }
+    catch {
+        process.stdout.write('gd (unknown version)\n');
+    }
+    process.exit(0);
+}
+const command = flags.positional[0];
+const subcommand = flags.positional[1];
+const extraArgs = flags.positional.slice(2);
+// --help with no command, or no command at all
+if (!command || (flags.help && !command)) {
+    printHelp();
+    process.exit(0);
+}
+// Per-command --help
+if (flags.help) {
+    printCommandHelp(command);
+    process.exit(0);
+}
+const cwd = flags.cwd || process.cwd();
+let classification = classifyCommand(command, subcommand);
+// Codex r23 P2: `gd execute-phase <N> --dry-run` should hit the tool
+// dry-run preview, not the agent execute path. Override the agent
+// classification when the user passes --dry-run on an agent command
+// that exposes a tool-side dry-run handler.
+const DRYRUN_TOOL_OVERRIDES = new Set(['execute-phase']);
+if (classification === 'agent' &&
+    DRYRUN_TOOL_OVERRIDES.has(command) &&
+    (extraArgs.includes('--dry-run') || flags.passthrough.includes('--dry-run'))) {
+    classification = 'tool';
+}
+if (classification === 'tool') {
+    const result = runToolCommand(command, subcommand, extraArgs, flags.json, cwd, flags.passthrough);
+    if (result.stdout)
+        process.stdout.write(result.stdout);
+    if (result.stderr)
+        process.stderr.write(result.stderr);
+    process.exit(result.exitCode);
+}
+else if (classification === 'agent') {
+    const { detectBackend } = require('../lib/backend');
+    const backend = flags.backend || detectBackend(cwd);
+    runAgentCommand(command, flags.positional.slice(1), {
+        cwd,
+        backend,
+        json: flags.json,
+        verbose: flags.verbose,
+        model: flags.model,
+    });
+}
+else {
+    process.stderr.write(`Unknown command: ${command}\nRun "gd --help" for usage.\n`);
+    process.exit(1);
+}
+function printHelp() {
+    process.stdout.write(`gd — Get Research Done CLI
+
+Usage: gd <command> [args] [--json] [--help] [--version]
+
+Hero verbs (the closed loop):
+  init                 Bootstrap a new R&D project from a template
+  plan-phase <N>       Compose PLAN.md (Ouroboros context auto-injected)
+  execute-phase <N>    Run plans (wave-parallel + worktree-isolated)
+  verify-phase <N>     Reflection-loop verifier with Evidence Standard
+  autopilot            Run N phases end-to-end (the closed loop)
+  evolve               Autonomous self-improvement loop
+  health               Drift score + blockers + Ouroboros status
+  think                One-shot project briefing aggregating all primitives
+  singularity          % of recent LOC authored by gd evolve itself
+
+Workflow:
+  new-milestone        Start a new milestone cycle
+  autoplan             Auto-generate milestones from discoveries
+  progress             Show project progress
+  resume-project       Restore project context
+  pause-work           Save work state for later
+  quick                Execute small ad-hoc tasks
+
+Research:
+  survey <topic>       SoTA landscape scan
+  deep-dive <paper>    Paper deep analysis
+  compare-methods      Compare research methods
+  feasibility <topic>  Paper-to-production gap analysis
+
+Planning:
+  product-plan         Product-level planning
+  discuss-phase <N>    Brainstorm before planning
+  add-phase            Add a new phase
+  insert-phase         Insert phase between existing ones
+  remove-phase         Remove an unstarted phase
+
+Evaluation:
+  assess-baseline      Current performance baseline
+  eval-report <N>      Collect and analyze results
+  iterate <N>          Iteration loop on failed metrics
+  verify-work          Validate features with metrics
+
+Configuration:
+  settings             Configure workflow settings
+  principles           Create/edit project principles
+  discover [area]      Discover codebase standards
+  tracker-setup        Configure issue tracker
+
+Tools (deterministic, fast):
+  state <sub>          State management
+  verify <sub>         Verification suite (incl. \`verify mechanical\`)
+  phase <sub>          Phase lifecycle ops
+  scaffold <sub>       Directory scaffolding
+  frontmatter <sub>    YAML frontmatter CRUD
+  tracker <sub>        Issue tracker sync
+  roadmap <sub>        Roadmap queries
+  init <sub>           Workflow init contexts (internal)
+  version              Print version
+  phases               List all phases
+
+Ouroboros primitives (see docs/ouroboros-loop.md):
+  dead-end <sub>       DEAD-ENDS.md registry CRUD + promote-from-phase
+  genome <sub>         GENOME.md init / show / snapshot
+  plan-tournament      Score candidate PLAN.md files
+  scan                 Prompt-injection scanner
+
+Auxiliary (run \`gd <cmd> --help\` for details):
+  diagnose, blame, budget, impact, freshness, rollback, estimate,
+  estimate-phase, forecast-phase, check-plans, check-assumptions,
+  deps, deps-risk, knowledge, knowhow, eval, tail, watch,
+  research-gaps, import-knowhow, import-knowledge, export-research,
+  import-research, metrics
+
+Note: dashboard, health-check, coverage-report, phase-time-budget,
+todo-duplicates, markdown-split, and setup are DEPRECATED — see
+docs/DEPRECATIONS.md for the v0.4.x trim plan.
+
+Global Flags:
+  --json               Machine-parseable JSON output
+  --help               Show help text
+  --verbose            Extended output
+  --version            Print version and exit
+  --cwd <path>         Override working directory
+  --backend <id>       Force a specific backend (agent commands only)
+  --model <name>       Override model (agent commands only)
+
+Run "gd <command> --help" for command-specific usage.
+`);
+}
+function printCommandHelp(cmd) {
+    const resolvedCmd = cmd;
+    // Handle both bin/ (source) and dist/bin/ (compiled) locations
+    let cmdFile = join(__dirname, '..', 'commands', `${resolvedCmd}.md`);
+    if (!existsSync(cmdFile))
+        cmdFile = join(__dirname, '..', '..', 'commands', `${resolvedCmd}.md`);
+    if (existsSync(cmdFile)) {
+        const content = readFileSync(cmdFile, 'utf-8');
+        const match = content.match(/description:\s*(.+)/);
+        if (match) {
+            process.stdout.write(`gd ${cmd}: ${match[1].trim()}\n\n`);
+        }
+    }
+    process.stdout.write(`Usage: gd ${cmd} [args] [--json] [--verbose]\n`);
+}
+//# sourceMappingURL=gd.js.map

package/dist/bin/gd.js.map

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package/dist/bin/grd-manifest.d.ts

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+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=grd-manifest.d.ts.map

package/dist/bin/grd-manifest.d.ts.map

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

package/dist/bin/grd-manifest.js

@@ -0,0 +1,202 @@
+#!/usr/bin/env node
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+/**
+ * GRD Manifest — SHA256-based file tracking for self-update system
+ *
+ * Usage: node grd-manifest.js <command>
+ *
+ * Commands:
+ *   generate                    Generate grd-file-manifest.json with SHA256 hashes
+ *   detect                      Detect local modifications vs manifest
+ *   save-patches [--dir path]   Save modified files to grd-local-patches/
+ *   load-patches [--dir path]   Read patch backup metadata
+ */
+const fs = require('fs');
+const path = require('path');
+const crypto = require('crypto');
+const MANIFEST_FILE = 'grd-file-manifest.json';
+const PATCH_DIR = 'grd-local-patches';
+const BACKUP_META = 'backup-meta.json';
+// Files/dirs to exclude from manifest
+const EXCLUDE = new Set([
+    MANIFEST_FILE,
+    PATCH_DIR,
+    '.git',
+    'node_modules',
+    '.DS_Store',
+]);
+// ─── Helpers ─────────────────────────────────────────────────────────────────
+function getPluginRoot() {
+    return path.dirname(__dirname);
+}
+function sha256(filePath) {
+    const content = fs.readFileSync(filePath);
+    return crypto.createHash('sha256').update(content).digest('hex');
+}
+function walkDir(dir, base) {
+    const results = [];
+    const entries = fs.readdirSync(dir, { withFileTypes: true });
+    for (const entry of entries) {
+        if (EXCLUDE.has(entry.name))
+            continue;
+        const fullPath = path.join(dir, entry.name);
+        const relPath = path.relative(base, fullPath);
+        if (entry.isDirectory()) {
+            results.push(...walkDir(fullPath, base));
+        }
+        else if (entry.isFile()) {
+            results.push(relPath);
+        }
+    }
+    return results.sort();
+}
+function readVersion(pluginRoot) {
+    const versionFile = path.join(pluginRoot, 'VERSION');
+    if (fs.existsSync(versionFile)) {
+        return fs.readFileSync(versionFile, 'utf-8').trim();
+    }
+    return 'unknown';
+}
+// ─── Commands ────────────────────────────────────────────────────────────────
+function generateManifest(pluginRoot) {
+    const files = walkDir(pluginRoot, pluginRoot);
+    const hashes = {};
+    for (const file of files) {
+        const fullPath = path.join(pluginRoot, file);
+        hashes[file] = sha256(fullPath);
+    }
+    const manifest = {
+        version: readVersion(pluginRoot),
+        timestamp: new Date().toISOString(),
+        file_count: Object.keys(hashes).length,
+        files: hashes,
+    };
+    const manifestPath = path.join(pluginRoot, MANIFEST_FILE);
+    fs.writeFileSync(manifestPath, JSON.stringify(manifest, null, 2) + '\n', 'utf-8');
+    return manifest;
+}
+function detectModifications(pluginRoot) {
+    const manifestPath = path.join(pluginRoot, MANIFEST_FILE);
+    if (!fs.existsSync(manifestPath)) {
+        return {
+            error: 'No manifest found. Run: node bin/grd-manifest.js generate',
+            modifications: [],
+            additions: [],
+            deletions: [],
+            clean: false,
+        };
+    }
+    const manifest = JSON.parse(fs.readFileSync(manifestPath, 'utf-8'));
+    const modifications = [];
+    const additions = [];
+    const deletions = [];
+    // Check existing manifest entries
+    for (const [file, expectedHash] of Object.entries(manifest.files)) {
+        const fullPath = path.join(pluginRoot, file);
+        if (!fs.existsSync(fullPath)) {
+            deletions.push(file);
+        }
+        else {
+            const currentHash = sha256(fullPath);
+            if (currentHash !== expectedHash) {
+                modifications.push({
+                    file,
+                    expected: expectedHash,
+                    actual: currentHash,
+                });
+            }
+        }
+    }
+    // Check for new files
+    const currentFiles = walkDir(pluginRoot, pluginRoot);
+    for (const file of currentFiles) {
+        if (!manifest.files[file]) {
+            additions.push(file);
+        }
+    }
+    return {
+        version: manifest.version,
+        total_tracked: Object.keys(manifest.files).length,
+        modifications,
+        additions,
+        deletions,
+        clean: modifications.length === 0 && additions.length === 0 && deletions.length === 0,
+    };
+}
+function savePatches(pluginRoot, patchDirOverride) {
+    const detection = detectModifications(pluginRoot);
+    if (detection.error)
+        return { saved: false, error: detection.error };
+    if (detection.clean)
+        return { saved: false, reason: 'No modifications detected' };
+    const patchDir = patchDirOverride || path.join(pluginRoot, PATCH_DIR);
+    fs.mkdirSync(patchDir, { recursive: true });
+    const savedFiles = [];
+    for (const mod of detection.modifications) {
+        const srcPath = path.join(pluginRoot, mod.file);
+        const destPath = path.join(patchDir, mod.file);
+        fs.mkdirSync(path.dirname(destPath), { recursive: true });
+        fs.copyFileSync(srcPath, destPath);
+        savedFiles.push(mod.file);
+    }
+    const meta = {
+        from_version: detection.version,
+        timestamp: new Date().toISOString(),
+        files: savedFiles,
+        additions: detection.additions,
+        deletions: detection.deletions,
+    };
+    fs.writeFileSync(path.join(patchDir, BACKUP_META), JSON.stringify(meta, null, 2) + '\n', 'utf-8');
+    return { saved: true, patch_dir: patchDir, ...meta };
+}
+function loadPatches(pluginRoot, patchDirOverride) {
+    const patchDir = patchDirOverride || path.join(pluginRoot, PATCH_DIR);
+    const metaPath = path.join(patchDir, BACKUP_META);
+    if (!fs.existsSync(metaPath)) {
+        return { found: false, reason: `No patches found at ${patchDir}` };
+    }
+    const meta = JSON.parse(fs.readFileSync(metaPath, 'utf-8'));
+    return { found: true, patch_dir: patchDir, ...meta };
+}
+// ─── CLI ─────────────────────────────────────────────────────────────────────
+function main() {
+    const args = process.argv.slice(2);
+    const command = args[0];
+    const pluginRoot = getPluginRoot();
+    const dirIndex = args.indexOf('--dir');
+    const dirOverride = dirIndex !== -1 ? args[dirIndex + 1] : null;
+    let result;
+    switch (command) {
+        case 'generate':
+            result = generateManifest(pluginRoot);
+            console.log(JSON.stringify({
+                status: 'ok',
+                version: result.version,
+                file_count: result.file_count,
+                path: path.join(pluginRoot, MANIFEST_FILE),
+            }, null, 2));
+            break;
+        case 'detect':
+            result = detectModifications(pluginRoot);
+            console.log(JSON.stringify(result, null, 2));
+            if (result.error)
+                process.exit(1);
+            break;
+        case 'save-patches':
+            result = savePatches(pluginRoot, dirOverride);
+            console.log(JSON.stringify(result, null, 2));
+            if (result.error)
+                process.exit(1);
+            break;
+        case 'load-patches':
+            result = loadPatches(pluginRoot, dirOverride);
+            console.log(JSON.stringify(result, null, 2));
+            break;
+        default:
+            console.error('Usage: node grd-manifest.js <generate|detect|save-patches|load-patches>');
+            process.exit(1);
+    }
+}
+main();
+//# sourceMappingURL=grd-manifest.js.map

package/dist/bin/grd-manifest.js.map

@@ -0,0 +1 @@
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package/dist/bin/grd-mcp-server.d.ts

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

package/dist/bin/grd-mcp-server.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"grd-mcp-server.d.ts","sourceRoot":"","sources":["../../bin/grd-mcp-server.ts"],"names":[],"mappings":""}

package/dist/bin/grd-mcp-server.js

@@ -0,0 +1,71 @@
+#!/usr/bin/env node
+'use strict';
+Object.defineProperty(exports, "__esModule", { value: true });
+const { McpServer, } = require('../lib/mcp-server');
+const server = new McpServer({ cwd: process.cwd() });
+let buffer = '';
+process.stdin.setEncoding('utf-8');
+process.stdin.on('data', (chunk) => {
+    buffer += chunk;
+    // Process complete lines
+    let newlineIdx;
+    while ((newlineIdx = buffer.indexOf('\n')) !== -1) {
+        const line = buffer.slice(0, newlineIdx).trim();
+        buffer = buffer.slice(newlineIdx + 1);
+        // Skip empty lines
+        if (!line)
+            continue;
+        let message;
+        try {
+            message = JSON.parse(line);
+        }
+        catch (_e) {
+            // Malformed JSON -- write parse error response
+            const errorResponse = {
+                jsonrpc: '2.0',
+                id: null,
+                error: { code: -32700, message: 'Parse error' },
+            };
+            process.stdout.write(JSON.stringify(errorResponse) + '\n');
+            continue;
+        }
+        const response = server.handleMessage(message);
+        // Notifications return null -- no response needed
+        if (response !== null && response !== undefined) {
+            // Handle both sync responses and async (Promise) responses
+            Promise.resolve(response).then((r) => {
+                if (r !== null && r !== undefined) {
+                    process.stdout.write(JSON.stringify(r) + '\n');
+                }
+            });
+        }
+    }
+});
+process.stdin.on('end', () => {
+    // Handle any remaining data in buffer
+    const remaining = buffer.trim();
+    if (remaining) {
+        try {
+            const message = JSON.parse(remaining);
+            const response = server.handleMessage(message);
+            Promise.resolve(response).then((r) => {
+                if (r !== null && r !== undefined) {
+                    process.stdout.write(JSON.stringify(r) + '\n');
+                }
+            });
+        }
+        catch (_e) {
+            const errorResponse = {
+                jsonrpc: '2.0',
+                id: null,
+                error: { code: -32700, message: 'Parse error' },
+            };
+            process.stdout.write(JSON.stringify(errorResponse) + '\n');
+        }
+    }
+    process.exit(0);
+});
+process.stdin.on('error', () => {
+    process.exit(0);
+});
+//# sourceMappingURL=grd-mcp-server.js.map

package/dist/bin/grd-mcp-server.js.map

@@ -0,0 +1 @@
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package/dist/bin/grd-tools.d.ts

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

package/dist/bin/grd-tools.d.ts.map

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