fix(#484): persist research decision from new-milestone to config

When user selects "Skip research" during /gsd:new-milestone, the choice
was not saved to .planning/config.json. Later, /gsd:plan-phase would
read the default (research: true) and spawn researchers anyway.

- Add `config-set` command to gsd-tools.js for setting nested config values
- Update new-milestone workflow to persist research choice after user decides

Closes #484

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

get-shit-done/bin/gsd-tools.js

@@ -609,6 +609,51 @@ function cmdConfigEnsureSection(cwd, raw) {
   }
 }
 
+function cmdConfigSet(cwd, keyPath, value, raw) {
+  const configPath = path.join(cwd, '.planning', 'config.json');
+
+  if (!keyPath) {
+    error('Usage: config-set <key.path> <value>');
+  }
+
+  // Parse value (handle booleans and numbers)
+  let parsedValue = value;
+  if (value === 'true') parsedValue = true;
+  else if (value === 'false') parsedValue = false;
+  else if (!isNaN(value) && value !== '') parsedValue = Number(value);
+
+  // Load existing config or start with empty object
+  let config = {};
+  try {
+    if (fs.existsSync(configPath)) {
+      config = JSON.parse(fs.readFileSync(configPath, 'utf-8'));
+    }
+  } catch (err) {
+    error('Failed to read config.json: ' + err.message);
+  }
+
+  // Set nested value using dot notation (e.g., "workflow.research")
+  const keys = keyPath.split('.');
+  let current = config;
+  for (let i = 0; i < keys.length - 1; i++) {
+    const key = keys[i];
+    if (current[key] === undefined || typeof current[key] !== 'object') {
+      current[key] = {};
+    }
+    current = current[key];
+  }
+  current[keys[keys.length - 1]] = parsedValue;
+
+  // Write back
+  try {
+    fs.writeFileSync(configPath, JSON.stringify(config, null, 2), 'utf-8');
+    const result = { updated: true, key: keyPath, value: parsedValue };
+    output(result, raw, `${keyPath}=${parsedValue}`);
+  } catch (err) {
+    error('Failed to write config.json: ' + err.message);
+  }
+}
+
 function cmdHistoryDigest(cwd, raw) {
   const phasesDir = path.join(cwd, '.planning', 'phases');
   const digest = { phases: {}, decisions: [], tech_stack: new Set() };
@@ -4279,6 +4324,11 @@ function main() {
       break;
     }
 
+    case 'config-set': {
+      cmdConfigSet(cwd, args[1], args[2], raw);
+      break;
+    }
+
     case 'history-digest': {
       cmdHistoryDigest(cwd, raw);
       break;

get-shit-done/workflows/new-milestone.md

@@ -88,6 +88,16 @@ AskUserQuestion: "Research the domain ecosystem for new features before defining
 - "Research first (Recommended)" — Discover patterns, features, architecture for NEW capabilities
 - "Skip research" — Go straight to requirements
 
+**Persist choice to config** (so future `/gsd:plan-phase` honors it):
+
+```bash
+# If "Research first": persist true
+node ~/.claude/get-shit-done/bin/gsd-tools.js config-set workflow.research true
+
+# If "Skip research": persist false
+node ~/.claude/get-shit-done/bin/gsd-tools.js config-set workflow.research false
+```
+
 **If "Research first":**
 
 ```