New worktrees are created without their submodules #7672

Closed
#7674
Closed
New worktrees are created without their submodules#7672
#7674

Description

@Brechard
Brechard
opened on Aug 20, 2026

Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.

Why it hurts

Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:

diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.

Probing the Agent SDK for available commands shows the gap directly:

cwdcommands
repository root98
new worktree88

Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.

Expected

A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.

Reproduce

  1. Use a repository with a submodule.
  2. Start a thread with "new worktree".
  3. The submodule path in the new worktree is empty.

Environment

macOS, git 2.x.

Metadata

Metadata

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No one assigned

    Labels

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      , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
       blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

      Skip to content
      New worktrees are created without their submodules #7672
      Closed
      #7674
      Closed
      New worktrees are created without their submodules#7672
      #7674
      Description
      @Brechard
      Brechard
      opened on Aug 20, 2026
      Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.
      Why it hurts
      Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:
      diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

      Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.
      Probing the Agent SDK for available commands shows the gap directly:
      cwdcommands
      repository root98
      new worktree88
      Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.
      Expected
      A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.
      Reproduce
      1. Use a repository with a submodule.
      2. Start a thread with "new worktree".
      3. The submodule path in the new worktree is empty.
      Environment
      macOS, git 2.x.
      Metadata
      Metadata
      Assignees
      No one assigned
        Labels
        No labels
        No labels
        Type
        No type
        Projects
        No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

          Skip to content
          New worktrees are created without their submodules #7672
          Closed
          #7674
          Closed
          New worktrees are created without their submodules#7672
          #7674
          Description
          @Brechard
          Brechard
          opened on Aug 20, 2026
          Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.
          Why it hurts
          Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:
          diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

          Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.
          Probing the Agent SDK for available commands shows the gap directly:
          cwdcommands
          repository root98
          new worktree88
          Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.
          Expected
          A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.
          Reproduce
          1. Use a repository with a submodule.
          2. Start a thread with "new worktree".
          3. The submodule path in the new worktree is empty.
          Environment
          macOS, git 2.x.
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

              Skip to content
              New worktrees are created without their submodules #7672
              Closed
              #7674
              Closed
              New worktrees are created without their submodules#7672
              #7674
              Description
              @Brechard
              Brechard
              opened on Aug 20, 2026
              Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.
              Why it hurts
              Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:
              diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

              Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.
              Probing the Agent SDK for available commands shows the gap directly:
              cwdcommands
              repository root98
              new worktree88
              Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.
              Expected
              A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.
              Reproduce
              1. Use a repository with a submodule.
              2. Start a thread with "new worktree".
              3. The submodule path in the new worktree is empty.
              Environment
              macOS, git 2.x.
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                No labels
                No labels
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions
                  
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

                  Skip to content
                  New worktrees are created without their submodules #7672
                  Closed
                  #7674
                  Closed
                  New worktrees are created without their submodules#7672
                  #7674
                  Description
                  @Brechard
                  Brechard
                  opened on Aug 20, 2026
                  Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.
                  Why it hurts
                  Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:
                  diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

                  Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.
                  Probing the Agent SDK for available commands shows the gap directly:
                  cwdcommands
                  repository root98
                  new worktree88
                  Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.
                  Expected
                  A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.
                  Reproduce
                  1. Use a repository with a submodule.
                  2. Start a thread with "new worktree".
                  3. The submodule path in the new worktree is empty.
                  Environment
                  macOS, git 2.x.
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
                    No labels
                    No labels
                    Type
                    No type
                    Projects
                    No projects
                      Milestone
                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                      Skip to content
                      New worktrees are created without their submodules #7672
                      Closed
                      #7674
                      Closed
                      New worktrees are created without their submodules#7672
                      #7674
                      Description
                      @Brechard
                      Brechard
                      opened on Aug 20, 2026
                      Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.
                      Why it hurts
                      Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:
                      diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

                      Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.
                      Probing the Agent SDK for available commands shows the gap directly:
                      cwdcommands
                      repository root98
                      new worktree88
                      Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.
                      Expected
                      A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.
                      Reproduce
                      1. Use a repository with a submodule.
                      2. Start a thread with "new worktree".
                      3. The submodule path in the new worktree is empty.
                      Environment
                      macOS, git 2.x.
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
                          Relationships
                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                          Skip to content
                          New worktrees are created without their submodules #7672
                          Closed
                          #7674
                          Closed
                          New worktrees are created without their submodules#7672
                          #7674
                          Description
                          @Brechard
                          Brechard
                          opened on Aug 20, 2026
                          Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.
                          Why it hurts
                          Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:
                          diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

                          Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.
                          Probing the Agent SDK for available commands shows the gap directly:
                          cwdcommands
                          repository root98
                          new worktree88
                          Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.
                          Expected
                          A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.
                          Reproduce
                          1. Use a repository with a submodule.
                          2. Start a thread with "new worktree".
                          3. The submodule path in the new worktree is empty.
                          Environment
                          macOS, git 2.x.
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
                            Projects
                            No projects
                              Milestone
                              No milestone
                              Relationships
                              None yet
                              Development
                              No branches or pull requests
                              Issue actions
                              
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

                              Skip to content
                              New worktrees are created without their submodules #7672
                              Closed
                              #7674
                              Closed
                              New worktrees are created without their submodules#7672
                              #7674
                              Description
                              @Brechard
                              Brechard
                              opened on Aug 20, 2026
                              Starting a thread with "new worktree" runs git worktree add, which never populates submodules. The worktree is missing whatever they contain, with no indication anything is absent.
                              Why it hurts
                              Repositories that keep shared agent tooling in a submodule lose it in every worktree. In my case .agents/shared is a submodule holding skills that .claude/skills/* symlinks into, so each new worktree had ten dangling symlinks:
                              diagnosing-bugs feature-across-repos fix-code git-worktrees re-release-version
resolve-pr-comments resolving-merge-conflicts ship updating-shared-agent-rules verify-local

                              Skill discovery skips an unreadable SKILL.md, so the skills simply vanish from the picker. Running one reported Unknown command, which is accurate but gives no hint that the cause is an unpopulated submodule.
                              Probing the Agent SDK for available commands shows the gap directly:
                              cwdcommands
                              repository root98
                              new worktree88
                              Same repo, same branch content; the 10 missing entries are exactly the submodule-backed skills.
                              Expected
                              A worktree should match a fresh checkout of the same ref. git submodule update --init --recursive after worktree add fixes it, and costs ~90 ms offline because the objects are normally already in the parent's .git/modules. It needs to stay best-effort — a first-ever clone needs the network, and an unreachable submodule should not fail thread creation.
                              Reproduce
                              1. Use a repository with a submodule.
                              2. Start a thread with "new worktree".
                              3. The submodule path in the new worktree is empty.
                              Environment
                              macOS, git 2.x.
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