diff --git a/get-shit-done/bin/gsd-tools.cjs b/get-shit-done/bin/gsd-tools.cjs
index a7cd70377..4ee194ec1 100755
--- a/get-shit-done/bin/gsd-tools.cjs
+++ b/get-shit-done/bin/gsd-tools.cjs
@@ -181,10 +181,6 @@ async function main() {
     cwd = worktreeRoot;
   }
 
-  // Multi-repo guard: if CWD is inside a sub-repo, walk up to the project root
-  // so .planning/ is read/written at the correct level.
-  cwd = findProjectRoot(cwd);
-
   const rawIndex = args.indexOf('--raw');
   const raw = rawIndex !== -1;
   if (rawIndex !== -1) args.splice(rawIndex, 1);
@@ -195,6 +191,17 @@ async function main() {
     error('Usage: gsd-tools <command> [args] [--raw] [--cwd <path>]\nCommands: state, resolve-model, find-phase, commit, verify-summary, verify, frontmatter, template, generate-slug, current-timestamp, list-todos, verify-path-exists, config-ensure-section, init');
   }
 
+  // Multi-repo guard: resolve project root for commands that read/write .planning/.
+  // Skip for pure-utility commands that don't touch .planning/ to avoid unnecessary
+  // filesystem traversal on every invocation.
+  const SKIP_ROOT_RESOLUTION = new Set([
+    'generate-slug', 'current-timestamp', 'verify-path-exists',
+    'verify-summary', 'template', 'frontmatter',
+  ]);
+  if (!SKIP_ROOT_RESOLUTION.has(command)) {
+    cwd = findProjectRoot(cwd);
+  }
+
   switch (command) {
     case 'state': {
       const subcommand = args[1];
diff --git a/get-shit-done/bin/lib/commands.cjs b/get-shit-done/bin/lib/commands.cjs
index 27461c393..f0d95a3a0 100644
--- a/get-shit-done/bin/lib/commands.cjs
+++ b/get-shit-done/bin/lib/commands.cjs
@@ -298,6 +298,10 @@ function cmdCommitToSubrepo(cwd, message, files, raw) {
     }
   }
 
+  if (unmatched.length > 0) {
+    process.stderr.write(`Warning: ${unmatched.length} file(s) did not match any sub-repo prefix: ${unmatched.join(', ')}\n`);
+  }
+
   const repos = {};
   for (const [repo, repoFiles] of Object.entries(grouped)) {
     const repoCwd = path.join(cwd, repo);
diff --git a/get-shit-done/references/git-integration.md b/get-shit-done/references/git-integration.md
index 2b6a9b733..ef530533d 100644
--- a/get-shit-done/references/git-integration.md
+++ b/get-shit-done/references/git-integration.md
@@ -274,7 +274,7 @@ Set `commit_docs: false` so planning docs stay local and are not committed to an
 
 ### How It Works
 
-1. **Auto-detection:** During `/gsd:new-project`, directories with their own `.git` folder are detected and offered for selection as sub-repos.
+1. **Auto-detection:** During `/gsd:new-project`, directories with their own `.git` folder are detected and offered for selection as sub-repos. On subsequent runs, `loadConfig` auto-syncs the `sub_repos` list with the filesystem — adding newly created repos and removing deleted ones. This means `config.json` may be rewritten automatically when repos change on disk.
 2. **File grouping:** Code files are grouped by their sub-repo prefix (e.g., `backend/src/api/users.ts` belongs to the `backend/` repo).
 3. **Independent commits:** Each sub-repo receives its own atomic commit via `gsd-tools.cjs commit-to-subrepo`. File paths are made relative to the sub-repo root before staging.
 4. **Planning stays local:** The `.planning/` directory is not committed; it acts as cross-repo coordination.