diff --git a/.changeset/kind-foxes-click.md b/.changeset/kind-foxes-click.md
new file mode 100644
index 000000000..ad82444f2
--- /dev/null
+++ b/.changeset/kind-foxes-click.md
@@ -0,0 +1,5 @@
+---
+type: Added
+pr: 3522
+---
+**`gsd-sdk query commit --files` gains `--respect-staged` opt-in** — pass `--respect-staged` to skip the automatic `git add` step and commit only what is already staged within the requested pathspec. Callers using `git add -p` to stage individual hunks no longer have their partial staging silently overwritten. Without the flag, default behavior is unchanged (#3061 invariant preserved under both modes).
diff --git a/docs/CLI-TOOLS.md b/docs/CLI-TOOLS.md
index 505b5807d..1732ee3a8 100644
--- a/docs/CLI-TOOLS.md
+++ b/docs/CLI-TOOLS.md
@@ -422,11 +422,13 @@ node gsd-tools.cjs audit-open [--json]
node gsd-tools.cjs from-gsd2 [--path
] [--force] [--dry-run]
# Git commit with config checks
-node gsd-tools.cjs commit [--files f1 f2] [--amend] [--no-verify]
+node gsd-tools.cjs commit [--files f1 f2] [--amend] [--no-verify] [--respect-staged]
```
> `--no-verify`: Skips pre-commit hooks. Used by parallel executor agents during wave-based execution to avoid build lock contention (e.g., cargo lock fights in Rust projects). The orchestrator runs hooks once after each wave completes. Do not use `--no-verify` during sequential execution — let hooks run normally.
+> `--files ` **staging behaviour**: by default, `--files` runs `git add -- ` for each named file before committing. This overwrites any per-hunk staging set up via `git add -p`. Pass `--respect-staged` to skip the `git add` step and commit only what is already in the index within the requested pathspec. If nothing is staged within that scope, the command returns `{ committed: false, reason: 'nothing staged' }` without error. The trailing `-- ` pathspec on the commit is applied under both modes, so files staged outside the `--files` scope are never included (#3061 invariant).
+
# Web search (requires Brave API key)
node gsd-tools.cjs websearch [--limit N] [--freshness day|week|month]
```
diff --git a/sdk/src/query/QUERY-HANDLERS.md b/sdk/src/query/QUERY-HANDLERS.md
index b6189e3c6..1b936abb6 100644
--- a/sdk/src/query/QUERY-HANDLERS.md
+++ b/sdk/src/query/QUERY-HANDLERS.md
@@ -298,7 +298,7 @@ Disposition: **Registered** = handled in `createRegistry()` under the listed SDK
| `state` (subcommands) | `state.load`, `state.json`, `state.get`, `state.update`, `state.patch`, … | Registered | Dotted and `state …` space aliases in `index.ts`. |
| `resolve-model` | `resolve-model` | Registered | |
| `find-phase` | `find-phase` | Registered | Golden: subset parity (see above). |
-| `commit`, `check-commit`, `commit-to-subrepo` | `commit`, `check-commit`, `commit-to-subrepo` | Registered | |
+| `commit`, `check-commit`, `commit-to-subrepo` | `commit`, `check-commit`, `commit-to-subrepo` | Registered | `commit`: `--files` re-stages full files by default; use `--respect-staged` to skip `git add` and commit only what is already staged within the pathspec (#3522). |
| `verify-summary` | `verify-summary`, `verify.summary`, `verify summary` | Registered | |
| `template` | `template.fill`, `template.select`, … | Registered | |
| `frontmatter` | `frontmatter.get`, `frontmatter.set`, … | Registered | |
diff --git a/sdk/src/query/commit.test.ts b/sdk/src/query/commit.test.ts
index 96606c85a..f5ba9bab9 100644
--- a/sdk/src/query/commit.test.ts
+++ b/sdk/src/query/commit.test.ts
@@ -339,3 +339,124 @@ describe('commit input validation and option safety (#3061)', () => {
expect(committed).toContain(dashName);
});
});
+
+// ─── --respect-staged flag (#3522) ────────────────────────────────────────
+//
+// When --respect-staged is passed:
+// 1. The git add loop is skipped entirely — partial (per-hunk) staging is
+// preserved rather than overwritten by a full `git add -- `.
+// 2. If nothing is staged within the requested pathspec, the handler
+// returns { committed: false, reason: 'nothing staged' } without error.
+// 3. The #3061 invariant still holds: files staged *outside* --files
+// do not appear in the commit (trailing -- pathspec still applied).
+// 4. Without --respect-staged, --files re-stages the full file as before
+// (back-compat: partial staging is overwritten).
+
+describe('commit --respect-staged (#3522)', () => {
+ // Each test needs an existing HEAD so we can create tracked files and
+ // simulate `git add -p` style partial staging.
+ beforeEach(async () => {
+ await writeFile(join(tmpDir, 'README.md'), 'init\n');
+ execSync('git add README.md', { cwd: tmpDir, stdio: 'pipe' });
+ execSync('git commit -m "init"', { cwd: tmpDir, stdio: 'pipe' });
+ await writeFile(
+ join(tmpDir, '.planning', 'config.json'),
+ JSON.stringify({ commit_docs: true }),
+ );
+ });
+
+ it('commits only the pre-staged file when --respect-staged is passed (simulated git add -p)', async () => {
+ const { commit } = await import('./commit.js');
+
+ // Simulate a `git add -p` scenario using two files:
+ // - staged-hunk.ts: the hunk the operator chose to stage (staged beforehand)
+ // - unstaged-hunk.ts: the hunk the operator left out of the index
+ // Both paths are listed in --files. Without --respect-staged the handler
+ // would git add both, committing all working-tree changes. With
+ // --respect-staged it must commit only what is already in the index.
+ await writeFile(join(tmpDir, 'staged-hunk.ts'), '// selected hunk\nconst a = 1;\n');
+ await writeFile(join(tmpDir, 'unstaged-hunk.ts'), '// skipped hunk\nconst b = 2;\n');
+
+ // Stage only the selected hunk — the skipped hunk stays in the work tree.
+ execSync('git add staged-hunk.ts', { cwd: tmpDir, stdio: 'pipe' });
+
+ const result = await commit(
+ ['feat: partial hunk commit', '--files', 'staged-hunk.ts', 'unstaged-hunk.ts', '--respect-staged'],
+ tmpDir,
+ );
+ expect((result.data as { committed: boolean }).committed).toBe(true);
+
+ const committedFiles = execSync('git show --name-only --format= HEAD', { cwd: tmpDir, encoding: 'utf-8' })
+ .trim()
+ .split('\n')
+ .filter(Boolean);
+ // Only the pre-staged hunk must appear in the commit.
+ expect(committedFiles).toContain('staged-hunk.ts');
+ expect(committedFiles).not.toContain('unstaged-hunk.ts');
+ });
+
+ it('returns { committed: false, reason: "nothing staged" } when --respect-staged has nothing staged in pathspec', async () => {
+ const { commit } = await import('./commit.js');
+
+ // Create a file but do NOT stage it.
+ await writeFile(join(tmpDir, 'unstaged.ts'), '// not staged\n');
+
+ const result = await commit(
+ ['feat: should not commit', '--files', 'unstaged.ts', '--respect-staged'],
+ tmpDir,
+ );
+ expect((result.data as { committed: boolean }).committed).toBe(false);
+ expect((result.data as { reason: string }).reason).toBe('nothing staged');
+ });
+
+ it('files staged outside --files pathspec are excluded under --respect-staged (#3061 invariant)', async () => {
+ const { commit } = await import('./commit.js');
+
+ // Stage an "in-scope" file and an "out-of-scope" file.
+ await writeFile(join(tmpDir, 'in-scope.ts'), '// in scope\n');
+ await writeFile(join(tmpDir, 'out-of-scope.ts'), '// out of scope\n');
+ execSync('git add in-scope.ts out-of-scope.ts', { cwd: tmpDir, stdio: 'pipe' });
+
+ // --files only names in-scope.ts. --respect-staged skips git add.
+ const result = await commit(
+ ['feat: scoped commit', '--files', 'in-scope.ts', '--respect-staged'],
+ tmpDir,
+ );
+ expect((result.data as { committed: boolean }).committed).toBe(true);
+
+ const committedFiles = execSync('git show --name-only --format= HEAD', { cwd: tmpDir, encoding: 'utf-8' })
+ .trim()
+ .split('\n')
+ .filter(Boolean);
+ expect(committedFiles).toContain('in-scope.ts');
+ expect(committedFiles).not.toContain('out-of-scope.ts');
+
+ // out-of-scope.ts must remain staged (not committed, not lost).
+ const staged = execSync('git diff --cached --name-only', { cwd: tmpDir, encoding: 'utf-8' }).trim();
+ expect(staged).toContain('out-of-scope.ts');
+ });
+
+ it('without --respect-staged, --files re-stages the full file even when partially pre-staged (back-compat)', async () => {
+ const { commit } = await import('./commit.js');
+
+ // Write a file, land it, then modify it in working tree without staging.
+ await writeFile(join(tmpDir, 'full-file.ts'), '// original\n');
+ execSync('git add full-file.ts', { cwd: tmpDir, stdio: 'pipe' });
+ execSync('git commit -m "land file"', { cwd: tmpDir, stdio: 'pipe' });
+
+ // Unstaged modification in the working tree.
+ await writeFile(join(tmpDir, 'full-file.ts'), '// modified in working tree\n');
+
+ // Without --respect-staged, --files full-file.ts should run git add and
+ // stage the full working-tree content before committing.
+ const result = await commit(
+ ['feat: full restage', '--files', 'full-file.ts'],
+ tmpDir,
+ );
+ expect((result.data as { committed: boolean }).committed).toBe(true);
+
+ // The full working-tree change must be in the commit.
+ const diff = execSync('git show HEAD -- full-file.ts', { cwd: tmpDir, encoding: 'utf-8' });
+ expect(diff).toContain('// modified in working tree');
+ });
+});
diff --git a/sdk/src/query/commit.ts b/sdk/src/query/commit.ts
index 0e494d37a..8d1f702e7 100644
--- a/sdk/src/query/commit.ts
+++ b/sdk/src/query/commit.ts
@@ -91,7 +91,19 @@ export function sanitizeCommitMessage(text: string): string {
* Checks commit_docs config (unless --force), sanitizes message,
* stages specified files (or all .planning/), and commits.
*
- * @param args - args[0]=message, remaining=file paths or flags (--force, --amend, --no-verify)
+ * By default, `--files ` runs `git add -- ` for each named file
+ * before committing. This means any per-hunk staging set up via `git add -p`
+ * is **overwritten** by a full re-stage of the file's working-tree content.
+ *
+ * Pass `--respect-staged` to skip the `git add` step entirely. The handler
+ * will commit only what is already staged within the requested pathspec. If
+ * nothing is staged within that scope, the handler returns
+ * `{ committed: false, reason: 'nothing staged' }` without error. The #3061
+ * leak-prevention invariant still holds: the trailing `-- ` pathspec
+ * on the commit ensures files staged outside `--files ` are excluded.
+ *
+ * @param args - args[0]=message, remaining=file paths or flags
+ * (--force, --amend, --no-verify, --respect-staged)
* @param projectDir - Project root directory
* @returns QueryResult with commit result
*/
@@ -102,10 +114,11 @@ export const commit: QueryHandler = async (args, projectDir, workstream) => {
const hasForce = allArgs.includes('--force');
const hasAmend = allArgs.includes('--amend');
const hasNoVerify = allArgs.includes('--no-verify');
+ const hasRespectStaged = allArgs.includes('--respect-staged');
const filesIndex = allArgs.indexOf('--files');
const endIndex = filesIndex !== -1 ? filesIndex : allArgs.length;
// CodeRabbit #6: don't strip arbitrary `--foo` tokens from commit messages
- const knownFlags = new Set(['--force', '--amend', '--no-verify']);
+ const knownFlags = new Set(['--force', '--amend', '--no-verify', '--respect-staged']);
const messageArgs = allArgs.slice(0, endIndex).filter(a => !knownFlags.has(a));
const message = messageArgs.join(' ') || undefined;
const filePaths =
@@ -142,30 +155,60 @@ export const commit: QueryHandler = async (args, projectDir, workstream) => {
// Compute pathspec once: the handler commits exactly the paths it staged,
// never anything that was pre-staged externally (#3061).
const pathsToCommit = filePaths.length > 0 ? filePaths : ['.planning/'];
- for (const file of pathsToCommit) {
- // The `--` separator keeps any path that starts with `-` from being
- // interpreted as a git option (e.g. a file literally named `-A`).
- const addResult = execGit(projectDir, ['add', '--', file]);
- if (addResult.exitCode !== 0) {
- return { data: { committed: false, reason: addResult.stderr || `failed to stage ${file}`, exitCode: addResult.exitCode } };
+
+ // When --respect-staged is set, skip re-staging so that per-hunk staging
+ // from `git add -p` is preserved. Without the flag, run git add for each
+ // path (default behavior, back-compat).
+ if (!hasRespectStaged) {
+ for (const file of pathsToCommit) {
+ // The `--` separator keeps any path that starts with `-` from being
+ // interpreted as a git option (e.g. a file literally named `-A`).
+ const addResult = execGit(projectDir, ['add', '--', file]);
+ if (addResult.exitCode !== 0) {
+ return { data: { committed: false, reason: addResult.stderr || `failed to stage ${file}`, exitCode: addResult.exitCode } };
+ }
}
}
// Check if anything is staged within the pathspec we're about to commit.
- const diffResult = execGit(projectDir, ['diff', '--cached', '--name-only', '--', ...pathsToCommit]);
- const stagedFiles = diffResult.stdout ? diffResult.stdout.split('\n').filter(Boolean) : [];
+ // When --respect-staged is set the caller may list paths that git doesn't
+ // know yet (e.g. untracked files the operator intentionally skipped via
+ // `git add -p`). Passing those unknown paths directly as a git pathspec
+ // causes `git diff --cached` to exit non-zero with "pathspec did not match".
+ // To avoid that, get all staged files and filter by the requested paths in
+ // TypeScript instead.
+ const stagedFiles: string[] = (() => {
+ if (hasRespectStaged) {
+ const allStaged = execGit(projectDir, ['diff', '--cached', '--name-only']);
+ const allStagedFiles = allStaged.stdout ? allStaged.stdout.split('\n').filter(Boolean) : [];
+ // Build a Set of the requested paths for O(1) lookup.
+ const pathSet = new Set(pathsToCommit);
+ // For directory entries (e.g. '.planning/'), match by prefix.
+ return allStagedFiles.filter(f =>
+ pathSet.has(f) || pathsToCommit.some(p => p.endsWith('/') && f.startsWith(p)),
+ );
+ }
+ const diffResult = execGit(projectDir, ['diff', '--cached', '--name-only', '--', ...pathsToCommit]);
+ return diffResult.stdout ? diffResult.stdout.split('\n').filter(Boolean) : [];
+ })();
if (stagedFiles.length === 0) {
return { data: { committed: false, reason: 'nothing staged' } };
}
- // Build commit command. The trailing `-- pathsToCommit` ensures the commit
- // captures only files within the requested scope, even when the caller's
- // index already had unrelated entries staged before this handler ran.
+ // Build commit command. The trailing pathspec ensures the commit captures
+ // only files within the requested scope (#3061 invariant).
+ //
+ // For the default path: use `pathsToCommit` (the caller's requested scope).
+ // For --respect-staged: use `stagedFiles` (the exact set already in the
+ // index within scope). This avoids git rejecting the commit when the caller
+ // listed paths that are not yet known to git (e.g. skipped hunks from
+ // `git add -p` that were intentionally left unstaged).
+ const commitPathspec = hasRespectStaged ? stagedFiles : pathsToCommit;
const commitArgs: string[] = hasAmend
? ['commit', '--amend', '--no-edit']
: ['commit', '-m', sanitized ?? ''];
if (hasNoVerify) commitArgs.push('--no-verify');
- commitArgs.push('--', ...pathsToCommit);
+ commitArgs.push('--', ...commitPathspec);
const commitResult = execGit(projectDir, commitArgs);
if (commitResult.exitCode !== 0) {