diff --git a/get-shit-done/bin/lib/config.cjs b/get-shit-done/bin/lib/config.cjs
index 67fe5a6b9..fefb63c96 100644
--- a/get-shit-done/bin/lib/config.cjs
+++ b/get-shit-done/bin/lib/config.cjs
@@ -25,6 +25,7 @@ const VALID_CONFIG_KEYS = new Set([
   'git.branching_strategy', 'git.phase_branch_template', 'git.milestone_branch_template', 'git.quick_branch_template',
   'planning.commit_docs', 'planning.search_gitignored',
   'hooks.context_warnings',
+  'project_code', 'phase_naming',
 ]);
 
 /**
@@ -132,6 +133,8 @@ function buildNewProjectConfig(userChoices) {
     hooks: {
       context_warnings: true,
     },
+    project_code: null,
+    phase_naming: 'sequential',
     agent_skills: {},
   };
 
diff --git a/get-shit-done/bin/lib/core.cjs b/get-shit-done/bin/lib/core.cjs
index e509e849a..ebe19ac24 100644
--- a/get-shit-done/bin/lib/core.cjs
+++ b/get-shit-done/bin/lib/core.cjs
@@ -217,6 +217,7 @@ function loadConfig(cwd) {
     resolve_model_ids: false, // false: return alias as-is | true: map to full Claude model ID | "omit": return '' (runtime uses its default)
     context_window: 200000, // default 200k; set to 1000000 for Opus/Sonnet 4.6 1M models
     phase_naming: 'sequential', // 'sequential' (default, auto-increment) or 'custom' (arbitrary string IDs)
+    project_code: null, // optional short prefix for phase dirs (e.g., 'CK' → 'CK-01-foundation')
   };
 
   try {
@@ -308,6 +309,7 @@ function loadConfig(cwd) {
       resolve_model_ids: get('resolve_model_ids') ?? defaults.resolve_model_ids,
       context_window: get('context_window') ?? defaults.context_window,
       phase_naming: get('phase_naming') ?? defaults.phase_naming,
+      project_code: get('project_code') ?? defaults.project_code,
       model_overrides: parsed.model_overrides || null,
       agent_skills: parsed.agent_skills || {},
     };
@@ -619,8 +621,10 @@ function escapeRegex(value) {
 
 function normalizePhaseName(phase) {
   const str = String(phase);
+  // Strip optional project_code prefix (e.g., 'CK-01' → '01')
+  const stripped = str.replace(/^[A-Z]{1,6}-(?=\d)/, '');
   // Standard numeric phases: 1, 01, 12A, 12.1
-  const match = str.match(/^(\d+)([A-Z])?((?:\.\d+)*)/i);
+  const match = stripped.match(/^(\d+)([A-Z])?((?:\.\d+)*)/i);
   if (match) {
     const padded = match[1].padStart(2, '0');
     const letter = match[2] ? match[2].toUpperCase() : '';
@@ -632,8 +636,11 @@ function normalizePhaseName(phase) {
 }
 
 function comparePhaseNum(a, b) {
-  const pa = String(a).match(/^(\d+)([A-Z])?((?:\.\d+)*)/i);
-  const pb = String(b).match(/^(\d+)([A-Z])?((?:\.\d+)*)/i);
+  // Strip optional project_code prefix before comparing (e.g., 'CK-01-name' → '01-name')
+  const sa = String(a).replace(/^[A-Z]{1,6}-/, '');
+  const sb = String(b).replace(/^[A-Z]{1,6}-/, '');
+  const pa = sa.match(/^(\d+)([A-Z])?((?:\.\d+)*)/i);
+  const pb = sb.match(/^(\d+)([A-Z])?((?:\.\d+)*)/i);
   // If either is non-numeric (custom ID), fall back to string comparison
   if (!pa || !pb) return String(a).localeCompare(String(b));
   const intDiff = parseInt(pa[1], 10) - parseInt(pb[1], 10);
@@ -668,12 +675,17 @@ function searchPhaseInDir(baseDir, relBase, normalized) {
       if (d.startsWith(normalized)) return true;
       // For custom IDs like PROJ-42, match case-insensitively
       if (d.toUpperCase().startsWith(normalized.toUpperCase())) return true;
+      // Strip optional project_code prefix (e.g., 'CK-01-name' → '01-name') and retry
+      const stripped = d.replace(/^[A-Z]{1,6}-/, '');
+      if (stripped.startsWith(normalized)) return true;
+      if (stripped.toUpperCase().startsWith(normalized.toUpperCase())) return true;
       return false;
     });
     if (!match) return null;
 
-    // Extract phase number and name — supports both numeric (01-name) and custom (PROJ-42-name)
-    const dirMatch = match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
+    // Extract phase number and name — supports numeric (01-name), project-code-prefixed (CK-01-name), and custom (PROJ-42-name)
+    const dirMatch = match.match(/^(?:[A-Z]{1,6}-)(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
+      || match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
       || match.match(/^([A-Z][A-Z0-9]*(?:-[A-Z0-9]+)*)-(.+)/i)
       || [null, match, null];
     const phaseNumber = dirMatch ? dirMatch[1] : normalized;
diff --git a/get-shit-done/bin/lib/init.cjs b/get-shit-done/bin/lib/init.cjs
index d9ee54e42..0cb2a078f 100644
--- a/get-shit-done/bin/lib/init.cjs
+++ b/get-shit-done/bin/lib/init.cjs
@@ -108,6 +108,7 @@ function cmdInitExecutePhase(cwd, phase, raw) {
     // Branch name (pre-computed)
     branch_name: config.branching_strategy === 'phase' && phaseInfo
       ? config.phase_branch_template
+          .replace('{project}', config.project_code || '')
           .replace('{phase}', phaseInfo.phase_number)
           .replace('{slug}', phaseInfo.phase_slug || 'phase')
       : config.branching_strategy === 'milestone'
diff --git a/get-shit-done/bin/lib/phase.cjs b/get-shit-done/bin/lib/phase.cjs
index cfb9d3669..15c7409ce 100644
--- a/get-shit-done/bin/lib/phase.cjs
+++ b/get-shit-done/bin/lib/phase.cjs
@@ -163,13 +163,22 @@ function cmdFindPhase(cwd, phase, raw) {
     const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
     const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort((a, b) => comparePhaseNum(a, b));
 
-    const match = dirs.find(d => d.startsWith(normalized));
+    const match = dirs.find(d => {
+      if (d.startsWith(normalized)) return true;
+      if (d.toUpperCase().startsWith(normalized.toUpperCase())) return true;
+      // Strip optional project_code prefix (e.g., 'CK-01-name' → '01-name') and retry
+      const stripped = d.replace(/^[A-Z]{1,6}-/, '');
+      if (stripped.startsWith(normalized)) return true;
+      return false;
+    });
     if (!match) {
       output(notFound, raw, '');
       return;
     }
 
-    const dirMatch = match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
+    // Extract phase number — supports project-code-prefixed (CK-01-name), numeric (01-name), and custom IDs
+    const dirMatch = match.match(/^(?:[A-Z]{1,6}-)(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
+      || match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
     const phaseNumber = dirMatch ? dirMatch[1] : normalized;
     const phaseName = dirMatch && dirMatch[2] ? dirMatch[2] : null;
 
@@ -326,11 +335,15 @@ function cmdPhaseAdd(cwd, description, raw, customId) {
   let newPhaseId;
   let dirName;
 
+  // Optional project code prefix (e.g., 'CK' → 'CK-01-foundation')
+  const projectCode = config.project_code || '';
+  const prefix = projectCode ? `${projectCode}-` : '';
+
   if (customId || config.phase_naming === 'custom') {
     // Custom phase naming: use provided ID or generate from description
     newPhaseId = customId || slug.toUpperCase().replace(/-/g, '-');
     if (!newPhaseId) error('--id required when phase_naming is "custom"');
-    dirName = `${newPhaseId}-${slug}`;
+    dirName = `${prefix}${newPhaseId}-${slug}`;
   } else {
     // Sequential mode: find highest integer phase number (in current milestone only)
     const phasePattern = /#{2,4}\s*Phase\s+(\d+)[A-Z]?(?:\.\d+)*:/gi;
@@ -343,7 +356,7 @@ function cmdPhaseAdd(cwd, description, raw, customId) {
 
     newPhaseId = maxPhase + 1;
     const paddedNum = String(newPhaseId).padStart(2, '0');
-    dirName = `${paddedNum}-${slug}`;
+    dirName = `${prefix}${paddedNum}-${slug}`;
   }
 
   const dirPath = path.join(planningDir(cwd), 'phases', dirName);
@@ -410,7 +423,7 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
   try {
     const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
     const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
-    const decimalPattern = new RegExp(`^${normalizedBase}\\.(\\d+)`);
+    const decimalPattern = new RegExp(`^(?:[A-Z]{1,6}-)?${normalizedBase}\\.(\\d+)`);
     for (const dir of dirs) {
       const dm = dir.match(decimalPattern);
       if (dm) existingDecimals.push(parseInt(dm[1], 10));
@@ -419,7 +432,12 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
 
   const nextDecimal = existingDecimals.length === 0 ? 1 : Math.max(...existingDecimals) + 1;
   const decimalPhase = `${normalizedBase}.${nextDecimal}`;
-  const dirName = `${decimalPhase}-${slug}`;
+
+  // Optional project code prefix
+  const config = loadConfig(cwd);
+  const projectCode = config.project_code || '';
+  const prefix = projectCode ? `${projectCode}-` : '';
+  const dirName = `${prefix}${decimalPhase}-${slug}`;
   const dirPath = path.join(planningDir(cwd), 'phases', dirName);
 
   // Create directory with .gitkeep so git tracks empty folders
diff --git a/get-shit-done/templates/config.json b/get-shit-done/templates/config.json
index fd147b6f4..c629c22f4 100644
--- a/get-shit-done/templates/config.json
+++ b/get-shit-done/templates/config.json
@@ -40,5 +40,6 @@
   "hooks": {
     "context_warnings": true
   },
+  "project_code": null,
   "agent_skills": {}
 }
diff --git a/tests/phase.test.cjs b/tests/phase.test.cjs
index bbc0c004e..193d4b739 100644
--- a/tests/phase.test.cjs
+++ b/tests/phase.test.cjs
@@ -657,6 +657,92 @@ describe('phase add command', () => {
   });
 });
 
+// ─────────────────────────────────────────────────────────────────────────────
+// phase add with project_code prefix
+// ─────────────────────────────────────────────────────────────────────────────
+
+
+describe('phase add with project_code', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempProject();
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('prefixes phase directory with project_code', () => {
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ project_code: 'CK' })
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'ROADMAP.md'),
+      '# Roadmap v1.0\n\n### Phase 1: Foundation\n**Goal:** Setup\n\n---\n'
+    );
+
+    const result = runGsdTools('phase add User Dashboard', tmpDir, { HOME: tmpDir });
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.strictEqual(output.phase_number, 2, 'should be phase 2');
+    assert.ok(
+      fs.existsSync(path.join(tmpDir, '.planning', 'phases', 'CK-02-user-dashboard')),
+      'directory should have CK- prefix'
+    );
+  });
+
+  test('no prefix when project_code is null', () => {
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ project_code: null })
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'ROADMAP.md'),
+      '# Roadmap v1.0\n\n### Phase 1: Foundation\n**Goal:** Setup\n\n---\n'
+    );
+
+    const result = runGsdTools('phase add User Dashboard', tmpDir, { HOME: tmpDir });
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    assert.ok(
+      fs.existsSync(path.join(tmpDir, '.planning', 'phases', '02-user-dashboard')),
+      'directory should have no prefix'
+    );
+  });
+
+  test('find-phase resolves prefixed directories', () => {
+    const phaseDir = path.join(tmpDir, '.planning', 'phases', 'CK-01-foundation');
+    fs.mkdirSync(phaseDir, { recursive: true });
+    fs.writeFileSync(path.join(phaseDir, '01-01-PLAN.md'), '# Plan');
+
+    const result = runGsdTools('find-phase 01', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.strictEqual(output.found, true, 'should find prefixed phase');
+    assert.strictEqual(output.phase_number, '01', 'should extract numeric phase number');
+  });
+
+  test('phases list sorts prefixed directories correctly', () => {
+    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', 'CK-02-api'), { recursive: true });
+    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', 'CK-01-foundation'), { recursive: true });
+    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', 'CK-03-ui'), { recursive: true });
+
+    const result = runGsdTools('phases list', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.deepStrictEqual(
+      output.directories,
+      ['CK-01-foundation', 'CK-02-api', 'CK-03-ui'],
+      'prefixed phases should sort numerically'
+    );
+  });
+});
+
 // ─────────────────────────────────────────────────────────────────────────────
 // phase insert command
 // ─────────────────────────────────────────────────────────────────────────────