diff --git a/agents/gsd-code-fixer.md b/agents/gsd-code-fixer.md
index d856748e9c..7d1ac154ed 100644
--- a/agents/gsd-code-fixer.md
+++ b/agents/gsd-code-fixer.md
@@ -345,6 +345,7 @@ Use `gsd-sdk query commit` with conventional format (message first, then every s
 ```bash
 gsd-sdk query commit \
   "fix({padded_phase}): {finding_id} {short_description}" \
+  --files \
   {all_modified_files}
 ```
 
@@ -354,7 +355,7 @@ Examples:
 
 **Multiple files:** List ALL modified files after the message (space-separated):
 ```bash
-gsd-sdk query commit "fix(02): CR-01 ..." \
+gsd-sdk query commit "fix(02): CR-01 ..." --files \
   src/api/auth.ts src/types/user.ts tests/auth.test.ts
 ```
 
diff --git a/agents/gsd-debugger.md b/agents/gsd-debugger.md
index 185436fd69..0199d7d895 100644
--- a/agents/gsd-debugger.md
+++ b/agents/gsd-debugger.md
@@ -1168,7 +1168,7 @@ Root cause: {root_cause}"
 
 Then commit planning docs via CLI (respects `commit_docs` config automatically):
 ```bash
-gsd-sdk query commit "docs: resolve debug {slug}" .planning/debug/resolved/{slug}.md
+gsd-sdk query commit "docs: resolve debug {slug}" --files .planning/debug/resolved/{slug}.md
 ```
 
 **Append to knowledge base:**
@@ -1199,7 +1199,7 @@ Then append the entry:
 
 Commit the knowledge base update alongside the resolved session:
 ```bash
-gsd-sdk query commit "docs: update debug knowledge base with {slug}" .planning/debug/knowledge-base.md
+gsd-sdk query commit "docs: update debug knowledge base with {slug}" --files .planning/debug/knowledge-base.md
 ```
 
 Report completion and offer next steps.
diff --git a/agents/gsd-executor.md b/agents/gsd-executor.md
index dd8d60ef90..71d258f3d3 100644
--- a/agents/gsd-executor.md
+++ b/agents/gsd-executor.md
@@ -563,7 +563,7 @@ gsd-sdk query state.add-blocker "Blocker description"
 
 <final_commit>
 ```bash
-gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" \
+gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" --files \
   .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md .planning/REQUIREMENTS.md
 ```
 
diff --git a/agents/gsd-phase-researcher.md b/agents/gsd-phase-researcher.md
index 83baff8750..6f7df87c44 100644
--- a/agents/gsd-phase-researcher.md
+++ b/agents/gsd-phase-researcher.md
@@ -755,7 +755,7 @@ Write to: `$PHASE_DIR/$PADDED_PHASE-RESEARCH.md`
 ## Step 7: Commit Research (optional)
 
 ```bash
-gsd-sdk query commit "docs($PHASE): research phase domain" "$PHASE_DIR/$PADDED_PHASE-RESEARCH.md"
+gsd-sdk query commit "docs($PHASE): research phase domain" --files "$PHASE_DIR/$PADDED_PHASE-RESEARCH.md"
 ```
 
 ## Step 8: Return Structured Result
diff --git a/agents/gsd-planner.md b/agents/gsd-planner.md
index dc7e702a40..9a5a9a20d5 100644
--- a/agents/gsd-planner.md
+++ b/agents/gsd-planner.md
@@ -1136,7 +1136,7 @@ Plans:
 
 <step name="git_commit">
 ```bash
-gsd-sdk query commit "docs($PHASE): create phase plan" \
+gsd-sdk query commit "docs($PHASE): create phase plan" --files \
   .planning/phases/$PHASE-*/$PHASE-*-PLAN.md .planning/ROADMAP.md
 ```
 </step>
diff --git a/agents/gsd-research-synthesizer.md b/agents/gsd-research-synthesizer.md
index e9b9564dd2..16fc2f51d7 100644
--- a/agents/gsd-research-synthesizer.md
+++ b/agents/gsd-research-synthesizer.md
@@ -139,7 +139,7 @@ Write to `.planning/research/SUMMARY.md`
 The 4 parallel researcher agents write files but do NOT commit. You commit everything together.
 
 ```bash
-gsd-sdk query commit "docs: complete project research" .planning/research/
+gsd-sdk query commit "docs: complete project research" --files .planning/research/
 ```
 
 ## Step 8: Return Summary
diff --git a/agents/gsd-ui-researcher.md b/agents/gsd-ui-researcher.md
index 2efca92653..a64e53a5bb 100644
--- a/agents/gsd-ui-researcher.md
+++ b/agents/gsd-ui-researcher.md
@@ -292,7 +292,7 @@ Fill all sections. Write to `$PHASE_DIR/$PADDED_PHASE-UI-SPEC.md`.
 ## Step 6: Commit (optional)
 
 ```bash
-gsd-sdk query commit "docs($PHASE): UI design contract" "$PHASE_DIR/$PADDED_PHASE-UI-SPEC.md"
+gsd-sdk query commit "docs($PHASE): UI design contract" --files "$PHASE_DIR/$PADDED_PHASE-UI-SPEC.md"
 ```
 
 ## Step 7: Return Structured Result
diff --git a/commands/gsd/add-backlog.md b/commands/gsd/add-backlog.md
index ee6c4ea09d..1127553e32 100644
--- a/commands/gsd/add-backlog.md
+++ b/commands/gsd/add-backlog.md
@@ -54,7 +54,7 @@ the normal phase sequence and accumulate context over time.
 
 5. **Commit:**
    ```bash
-   gsd-sdk query commit "docs: add backlog item ${NEXT} — ${ARGUMENTS}" .planning/ROADMAP.md ".planning/phases/${NEXT}-${SLUG}/.gitkeep"
+   gsd-sdk query commit "docs: add backlog item ${NEXT} — ${ARGUMENTS}" --files .planning/ROADMAP.md ".planning/phases/${NEXT}-${SLUG}/.gitkeep"
    ```
 
 6. **Report:**
diff --git a/commands/gsd/review-backlog.md b/commands/gsd/review-backlog.md
index 0eb27b69a2..a8188caaac 100644
--- a/commands/gsd/review-backlog.md
+++ b/commands/gsd/review-backlog.md
@@ -47,7 +47,7 @@ milestone sequence or remove stale entries.
 
 6. **Commit changes:**
    ```bash
-   gsd-sdk query commit "docs: review backlog — promoted N, removed M" .planning/ROADMAP.md
+   gsd-sdk query commit "docs: review backlog — promoted N, removed M" --files .planning/ROADMAP.md
    ```
 
 7. **Report summary:**
diff --git a/commands/gsd/thread.md b/commands/gsd/thread.md
index 023b1590ee..ee10e54b03 100644
--- a/commands/gsd/thread.md
+++ b/commands/gsd/thread.md
@@ -83,7 +83,7 @@ When SUBCMD=close and SLUG is set (already sanitized):
 
 3. Commit:
    ```bash
-   gsd-sdk query commit "docs: resolve thread — {SLUG}" ".planning/threads/{SLUG}.md"
+   gsd-sdk query commit "docs: resolve thread — {SLUG}" --files ".planning/threads/{SLUG}.md"
    ```
 
 4. Print:
@@ -191,7 +191,7 @@ updated: {today ISO date}
 
 5. Commit:
    ```bash
-   gsd-sdk query commit "docs: create thread — ${ARGUMENTS}" ".planning/threads/${SLUG}.md"
+   gsd-sdk query commit "docs: create thread — ${ARGUMENTS}" --files ".planning/threads/${SLUG}.md"
    ```
 
 6. Report:
diff --git a/docs/zh-CN/references/git-integration.md b/docs/zh-CN/references/git-integration.md
index a840a0849c..7332d1cab9 100644
--- a/docs/zh-CN/references/git-integration.md
+++ b/docs/zh-CN/references/git-integration.md
@@ -51,7 +51,7 @@ Phases:
 提交内容：
 
 ```bash
-gsd-sdk query commit "docs: initialize [project-name] ([N] phases)" .planning/
+gsd-sdk query commit "docs: initialize [project-name] ([N] phases)" --files .planning/
 ```
 
 </format>
@@ -129,7 +129,7 @@ SUMMARY: .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md
 提交内容：
 
 ```bash
-gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" .planning/phases/XX-name/{phase}-{plan}-PLAN.md .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md
+gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" --files .planning/phases/XX-name/{phase}-{plan}-PLAN.md .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md
 ```
 
 **注意：** 代码文件不包含 - 已按任务提交。
@@ -149,7 +149,7 @@ Current: [task name]
 提交内容：
 
 ```bash
-gsd-sdk query commit "wip: [phase-name] paused at task [X]/[Y]" .planning/
+gsd-sdk query commit "wip: [phase-name] paused at task [X]/[Y]" --files .planning/
 ```
 
 </format>
diff --git a/docs/zh-CN/references/git-planning-commit.md b/docs/zh-CN/references/git-planning-commit.md
index 701ce35330..1a7618c37c 100644
--- a/docs/zh-CN/references/git-planning-commit.md
+++ b/docs/zh-CN/references/git-planning-commit.md
@@ -4,12 +4,12 @@
 
 ## 通过 CLI 提交
 
-先传提交说明，再传文件路径（位置参数）。`commit` 不要使用 `--files`（该标志仅用于 `commit-to-subrepo`）。
+先传提交说明，然后用 `--files` 显式传入文件路径。`commit` 与 `commit-to-subrepo` 都应使用 `--files` 来声明要提交的路径。
 
 对 `.planning/` 文件始终使用此方式 —— 它会自动处理 `commit_docs` 与 gitignore 检查：
 
 ```bash
-gsd-sdk query commit "docs({scope}): {description}" .planning/STATE.md .planning/ROADMAP.md
+gsd-sdk query commit "docs({scope}): {description}" --files .planning/STATE.md .planning/ROADMAP.md
 ```
 
 如果 `commit_docs` 为 `false` 或 `.planning/` 被 gitignore，CLI 会返回 `skipped`（带原因）。无需手动条件检查。
@@ -19,7 +19,7 @@ gsd-sdk query commit "docs({scope}): {description}" .planning/STATE.md .planning
 将 `.planning/` 文件变更合并到上次提交：
 
 ```bash
-gsd-sdk query commit "" .planning/codebase/*.md --amend
+gsd-sdk query commit "" --files .planning/codebase/*.md --amend
 ```
 
 ## 提交消息模式
diff --git a/docs/zh-CN/references/planning-config.md b/docs/zh-CN/references/planning-config.md
index 6ce0a30fdc..950f4d18e4 100644
--- a/docs/zh-CN/references/planning-config.md
+++ b/docs/zh-CN/references/planning-config.md
@@ -40,7 +40,7 @@
 
 ```bash
 # 提交时自动检查 commit_docs + gitignore：
-gsd-sdk query commit "docs: update state" .planning/STATE.md
+gsd-sdk query commit "docs: update state" --files .planning/STATE.md
 
 # 通过 state load 加载配置（返回 JSON）：
 INIT=$(gsd-sdk query state.load)
@@ -58,7 +58,7 @@ if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 **通过 CLI 提交（自动处理检查）：**
 
 ```bash
-gsd-sdk query commit "docs: update state" .planning/STATE.md
+gsd-sdk query commit "docs: update state" --files .planning/STATE.md
 ```
 
 CLI 在内部检查 `commit_docs` 配置和 gitignore 状态 —— 无需手动条件判断。
diff --git a/get-shit-done/references/autonomous-smart-discuss.md b/get-shit-done/references/autonomous-smart-discuss.md
index cefe5d603e..62156d278b 100644
--- a/get-shit-done/references/autonomous-smart-discuss.md
+++ b/get-shit-done/references/autonomous-smart-discuss.md
@@ -266,7 +266,7 @@ Write the file.
 **Commit:**
 
 ```bash
-gsd-sdk query commit "docs(${PADDED_PHASE}): smart discuss context" "${phase_dir}/${padded_phase}-CONTEXT.md"
+gsd-sdk query commit "docs(${PADDED_PHASE}): smart discuss context" --files "${phase_dir}/${padded_phase}-CONTEXT.md"
 ```
 
 Display confirmation:
diff --git a/get-shit-done/references/git-integration.md b/get-shit-done/references/git-integration.md
index 3ac371edbc..4b041b93c6 100644
--- a/get-shit-done/references/git-integration.md
+++ b/get-shit-done/references/git-integration.md
@@ -51,7 +51,7 @@ Phases:
 What to commit:
 
 ```bash
-gsd-sdk query commit "docs: initialize [project-name] ([N] phases)" .planning/
+gsd-sdk query commit "docs: initialize [project-name] ([N] phases)" --files .planning/
 ```
 
 </format>
@@ -133,7 +133,7 @@ SUMMARY: .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md
 What to commit:
 
 ```bash
-gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" .planning/phases/XX-name/{phase}-{plan}-PLAN.md .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md
+gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" --files .planning/phases/XX-name/{phase}-{plan}-PLAN.md .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md
 ```
 
 **Note:** Code files NOT included - already committed per-task.
@@ -153,7 +153,7 @@ Current: [task name]
 What to commit:
 
 ```bash
-gsd-sdk query commit "wip: [phase-name] paused at task [X]/[Y]" .planning/
+gsd-sdk query commit "wip: [phase-name] paused at task [X]/[Y]" --files .planning/
 ```
 
 </format>
diff --git a/get-shit-done/references/git-planning-commit.md b/get-shit-done/references/git-planning-commit.md
index 2609aa1aa9..7082bfedec 100644
--- a/get-shit-done/references/git-planning-commit.md
+++ b/get-shit-done/references/git-planning-commit.md
@@ -4,12 +4,12 @@ Commit planning artifacts via `gsd-sdk query commit`, which checks `commit_docs`
 
 ## Commit via CLI
 
-Pass the message first, then file paths (positional). Do not use `--files` for `commit` (that flag is only for `commit-to-subrepo`).
+Pass the message first, then file paths via `--files`. Both `commit` and `commit-to-subrepo` use `--files` to declare the paths to commit.
 
 Always use this for `.planning/` files — it handles `commit_docs` and gitignore checks automatically:
 
 ```bash
-gsd-sdk query commit "docs({scope}): {description}" .planning/STATE.md .planning/ROADMAP.md
+gsd-sdk query commit "docs({scope}): {description}" --files .planning/STATE.md .planning/ROADMAP.md
 ```
 
 The CLI will return `skipped` (with reason) if `commit_docs` is `false` or `.planning/` is gitignored. No manual conditional checks needed.
@@ -19,7 +19,7 @@ The CLI will return `skipped` (with reason) if `commit_docs` is `false` or `.pla
 To fold `.planning/` file changes into the previous commit:
 
 ```bash
-gsd-sdk query commit "" .planning/codebase/*.md --amend
+gsd-sdk query commit "" --files .planning/codebase/*.md --amend
 ```
 
 ## Commit Message Patterns
diff --git a/get-shit-done/references/planner-revision.md b/get-shit-done/references/planner-revision.md
index 7a7a796766..c37ea36635 100644
--- a/get-shit-done/references/planner-revision.md
+++ b/get-shit-done/references/planner-revision.md
@@ -55,7 +55,7 @@ Group by plan, dimension, severity.
 ### Step 6: Commit
 
 ```bash
-gsd-sdk query commit "fix($PHASE): revise plans based on checker feedback" .planning/phases/$PHASE-*/$PHASE-*-PLAN.md
+gsd-sdk query commit "fix($PHASE): revise plans based on checker feedback" --files .planning/phases/$PHASE-*/$PHASE-*-PLAN.md
 ```
 
 ### Step 7: Return Revision Summary
diff --git a/get-shit-done/references/planning-config.md b/get-shit-done/references/planning-config.md
index ad057b3d58..b4e5cca890 100644
--- a/get-shit-done/references/planning-config.md
+++ b/get-shit-done/references/planning-config.md
@@ -58,7 +58,7 @@ Configuration options for `.planning/` directory behavior.
 
 ```bash
 # Commit with automatic commit_docs + gitignore checks:
-gsd-sdk query commit "docs: update state" .planning/STATE.md
+gsd-sdk query commit "docs: update state" --files .planning/STATE.md
 
 # Load config via state load (returns JSON):
 INIT=$(gsd-sdk query state.load)
@@ -76,7 +76,7 @@ if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
 **Commit via CLI (handles checks automatically):**
 
 ```bash
-gsd-sdk query commit "docs: update state" .planning/STATE.md
+gsd-sdk query commit "docs: update state" --files .planning/STATE.md
 ```
 
 The CLI checks `commit_docs` config and gitignore status internally — no manual conditionals needed.
diff --git a/get-shit-done/workflows/add-todo.md b/get-shit-done/workflows/add-todo.md
index 439859da1e..6ae69f6854 100644
--- a/get-shit-done/workflows/add-todo.md
+++ b/get-shit-done/workflows/add-todo.md
@@ -121,7 +121,7 @@ If `.planning/STATE.md` exists:
 Commit the todo and any updated state:
 
 ```bash
-gsd-sdk query commit "docs: capture todo - [title]" .planning/todos/pending/[filename] .planning/STATE.md
+gsd-sdk query commit "docs: capture todo - [title]" --files .planning/todos/pending/[filename] .planning/STATE.md
 ```
 
 Tool respects `commit_docs` config and gitignore automatically.
diff --git a/get-shit-done/workflows/autonomous.md b/get-shit-done/workflows/autonomous.md
index 49fdf430c2..bac30e727d 100644
--- a/get-shit-done/workflows/autonomous.md
+++ b/get-shit-done/workflows/autonomous.md
@@ -249,7 +249,7 @@ None — discuss phase skipped.
 Commit the minimal context:
 
 ```bash
-gsd-sdk query commit "docs(${PADDED_PHASE}): auto-generated context (discuss skipped)" "${phase_dir}/${padded_phase}-CONTEXT.md"
+gsd-sdk query commit "docs(${PADDED_PHASE}): auto-generated context (discuss skipped)" --files "${phase_dir}/${padded_phase}-CONTEXT.md"
 ```
 
 Proceed to 3b.
diff --git a/get-shit-done/workflows/check-todos.md b/get-shit-done/workflows/check-todos.md
index 0180c404f6..760cb4bbbf 100644
--- a/get-shit-done/workflows/check-todos.md
+++ b/get-shit-done/workflows/check-todos.md
@@ -157,7 +157,7 @@ If todo was moved to done/, commit the change:
 
 ```bash
 git rm --cached .planning/todos/pending/[filename] 2>/dev/null || true
-gsd-sdk query commit "docs: start work on todo - [title]" .planning/todos/completed/[filename] .planning/STATE.md
+gsd-sdk query commit "docs: start work on todo - [title]" --files .planning/todos/completed/[filename] .planning/STATE.md
 ```
 
 Tool respects `commit_docs` config and gitignore automatically.
diff --git a/get-shit-done/workflows/cleanup.md b/get-shit-done/workflows/cleanup.md
index 534d33842c..d476e82b4b 100644
--- a/get-shit-done/workflows/cleanup.md
+++ b/get-shit-done/workflows/cleanup.md
@@ -124,7 +124,7 @@ Repeat for all milestones in the cleanup set.
 Commit the changes:
 
 ```bash
-gsd-sdk query commit "chore: archive phase directories from completed milestones" .planning/milestones/ .planning/phases/
+gsd-sdk query commit "chore: archive phase directories from completed milestones" --files .planning/milestones/ .planning/phases/
 ```
 
 </step>
diff --git a/get-shit-done/workflows/complete-milestone.md b/get-shit-done/workflows/complete-milestone.md
index a73b30563c..864227c23e 100644
--- a/get-shit-done/workflows/complete-milestone.md
+++ b/get-shit-done/workflows/complete-milestone.md
@@ -494,7 +494,7 @@ Append the extracted Backlog content verbatim to the end of the newly written RO
 **Safety commit — commit archive files BEFORE deleting any originals:**
 
 ```bash
-gsd-sdk query commit "chore: archive v[X.Y] milestone files" .planning/milestones/v[X.Y]-ROADMAP.md .planning/milestones/v[X.Y]-REQUIREMENTS.md .planning/milestones/v[X.Y]-MILESTONE-AUDIT.md .planning/MILESTONES.md .planning/PROJECT.md .planning/STATE.md .planning/ROADMAP.md
+gsd-sdk query commit "chore: archive v[X.Y] milestone files" --files .planning/milestones/v[X.Y]-ROADMAP.md .planning/milestones/v[X.Y]-REQUIREMENTS.md .planning/milestones/v[X.Y]-MILESTONE-AUDIT.md .planning/MILESTONES.md .planning/PROJECT.md .planning/STATE.md .planning/ROADMAP.md
 ```
 
 This creates a durable checkpoint in git history. If anything fails after this point, the working tree can be reconstructed from git.
@@ -563,7 +563,7 @@ If the "## Cross-Milestone Trends" section exists, update the tables with new da
 
 **Commit:**
 ```bash
-gsd-sdk query commit "docs: update retrospective for v${VERSION}" .planning/RETROSPECTIVE.md
+gsd-sdk query commit "docs: update retrospective for v${VERSION}" --files .planning/RETROSPECTIVE.md
 ```
 
 </step>
diff --git a/get-shit-done/workflows/diagnose-issues.md b/get-shit-done/workflows/diagnose-issues.md
index 808acbe511..d81cdafd78 100644
--- a/get-shit-done/workflows/diagnose-issues.md
+++ b/get-shit-done/workflows/diagnose-issues.md
@@ -179,7 +179,7 @@ Update status in frontmatter to "diagnosed".
 
 Commit the updated UAT.md:
 ```bash
-gsd-sdk query commit "docs({phase_num}): add root causes from diagnosis" ".planning/phases/XX-name/{phase_num}-UAT.md"
+gsd-sdk query commit "docs({phase_num}): add root causes from diagnosis" --files ".planning/phases/XX-name/{phase_num}-UAT.md"
 ```
 </step>
 
diff --git a/get-shit-done/workflows/discuss-phase-assumptions.md b/get-shit-done/workflows/discuss-phase-assumptions.md
index 1029bbbfb2..211b0b632d 100644
--- a/get-shit-done/workflows/discuss-phase-assumptions.md
+++ b/get-shit-done/workflows/discuss-phase-assumptions.md
@@ -552,7 +552,7 @@ Write file.
 Commit phase context and discussion log:
 
 ```bash
-gsd-sdk query commit "docs(${padded_phase}): capture phase context (assumptions mode)" "${phase_dir}/${padded_phase}-CONTEXT.md" "${phase_dir}/${padded_phase}-DISCUSSION-LOG.md"
+gsd-sdk query commit "docs(${padded_phase}): capture phase context (assumptions mode)" --files "${phase_dir}/${padded_phase}-CONTEXT.md" "${phase_dir}/${padded_phase}-DISCUSSION-LOG.md"
 ```
 
 Confirm: "Committed: docs(${padded_phase}): capture phase context (assumptions mode)"
@@ -570,7 +570,7 @@ gsd-sdk query state.record-session \
 Commit STATE.md:
 
 ```bash
-gsd-sdk query commit "docs(state): record phase ${PHASE} context session" .planning/STATE.md
+gsd-sdk query commit "docs(state): record phase ${PHASE} context session" --files .planning/STATE.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/discuss-phase.md b/get-shit-done/workflows/discuss-phase.md
index ac22e62969..57c67b4815 100644
--- a/get-shit-done/workflows/discuss-phase.md
+++ b/get-shit-done/workflows/discuss-phase.md
@@ -445,7 +445,7 @@ rm -f "${phase_dir}/${padded_phase}-DISCUSS-CHECKPOINT.json"
 
 Commit phase context and discussion log:
 ```bash
-gsd-sdk query commit "docs(${padded_phase}): capture phase context" "${phase_dir}/${padded_phase}-CONTEXT.md" "${phase_dir}/${padded_phase}-DISCUSSION-LOG.md"
+gsd-sdk query commit "docs(${padded_phase}): capture phase context" --files "${phase_dir}/${padded_phase}-CONTEXT.md" "${phase_dir}/${padded_phase}-DISCUSSION-LOG.md"
 ```
 
 Confirm: "Committed: docs(${padded_phase}): capture phase context"
@@ -459,7 +459,7 @@ gsd-sdk query state.record-session \
   --stopped-at "Phase ${PHASE} context gathered" \
   --resume-file "${phase_dir}/${padded_phase}-CONTEXT.md"
 
-gsd-sdk query commit "docs(state): record phase ${PHASE} context session" .planning/STATE.md
+gsd-sdk query commit "docs(state): record phase ${PHASE} context session" --files .planning/STATE.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/execute-phase.md b/get-shit-done/workflows/execute-phase.md
index 7fecfe7604..0a8d66e6eb 100644
--- a/get-shit-done/workflows/execute-phase.md
+++ b/get-shit-done/workflows/execute-phase.md
@@ -793,7 +793,7 @@ increases monotonically across waves. `{status}` is `complete` (success),
 
      # Only commit tracking files if they actually changed
      if ! git diff --quiet .planning/ROADMAP.md .planning/STATE.md 2>/dev/null; then
-       gsd-sdk query commit "docs(phase-${PHASE_NUMBER}): update tracking after wave ${N}" .planning/ROADMAP.md .planning/STATE.md
+       gsd-sdk query commit "docs(phase-${PHASE_NUMBER}): update tracking after wave ${N}" --files .planning/ROADMAP.md .planning/STATE.md
      fi
    elif [ "${TEST_EXIT}" -eq 124 ]; then
      echo "⚠ Skipping tracking update — test suite timed out. Plans remain in-progress. Run tests manually to confirm."
@@ -1143,7 +1143,7 @@ mv .planning/debug/{slug}.md .planning/debug/resolved/
 
 **6. Commit updated artifacts:**
 ```bash
-gsd-sdk query commit "docs(phase-${PARENT_PHASE}): resolve UAT gaps and debug sessions after ${PHASE_NUMBER} gap closure" .planning/phases/*${PARENT_PHASE}*/*-UAT.md .planning/debug/resolved/*.md
+gsd-sdk query commit "docs(phase-${PARENT_PHASE}): resolve UAT gaps and debug sessions after ${PHASE_NUMBER} gap closure" --files .planning/phases/*${PARENT_PHASE}*/*-UAT.md .planning/debug/resolved/*.md
 ```
 </step>
 
@@ -1386,7 +1386,7 @@ blocked: 0
 
 Commit the file:
 ```bash
-gsd-sdk query commit "test({phase_num}): persist human verification items as UAT" "{phase_dir}/{phase_num}-HUMAN-UAT.md"
+gsd-sdk query commit "test({phase_num}): persist human verification items as UAT" --files "{phase_dir}/{phase_num}-HUMAN-UAT.md"
 ```
 
 **Step B: Present to user:**
@@ -1458,7 +1458,7 @@ These items are tracked and will appear in `/gsd-progress` and `/gsd-audit-uat`.
 ```
 
 ```bash
-gsd-sdk query commit "docs(phase-{X}): complete phase execution" .planning/ROADMAP.md .planning/STATE.md .planning/REQUIREMENTS.md {phase_dir}/*-VERIFICATION.md
+gsd-sdk query commit "docs(phase-{X}): complete phase execution" --files .planning/ROADMAP.md .planning/STATE.md .planning/REQUIREMENTS.md {phase_dir}/*-VERIFICATION.md
 ```
 </step>
 
@@ -1508,7 +1508,7 @@ for TODO_FILE in "$PENDING_DIR"/*.md; do
 done
 
 if [ ${#CLOSED[@]} -gt 0 ]; then
-  gsd-sdk query commit "docs(phase-${PHASE_NUMBER}): auto-close ${#CLOSED[@]} todo(s) resolved by this phase" .planning/todos/completed/ .planning/STATE.md || true
+  gsd-sdk query commit "docs(phase-${PHASE_NUMBER}): auto-close ${#CLOSED[@]} todo(s) resolved by this phase" --files .planning/todos/completed/ .planning/STATE.md|| true
   echo "◆ Closed ${#CLOSED[@]} todo(s) resolved by Phase ${PHASE_NUMBER}:"
   for f in "${CLOSED[@]}"; do echo "  ✓ $f"; done
 fi
@@ -1533,7 +1533,7 @@ PROJECT.md falls behind silently over multiple phases.
 5. Commit the change:
 
 ```bash
-gsd-sdk query commit "docs(phase-{X}): evolve PROJECT.md after phase completion" .planning/PROJECT.md
+gsd-sdk query commit "docs(phase-{X}): evolve PROJECT.md after phase completion" --files .planning/PROJECT.md
 ```
 
 **Skip this step if** `.planning/PROJECT.md` does not exist.
diff --git a/get-shit-done/workflows/execute-plan.md b/get-shit-done/workflows/execute-plan.md
index 2766d7027b..268f449574 100644
--- a/get-shit-done/workflows/execute-plan.md
+++ b/get-shit-done/workflows/execute-plan.md
@@ -440,9 +440,9 @@ IS_WORKTREE=$([ -f .git ] && echo "true" || echo "false")
 
 # In parallel mode: exclude STATE.md and ROADMAP.md (orchestrator commits these)
 if [ "$IS_WORKTREE" = "true" ]; then
-  gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/REQUIREMENTS.md
+  gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" --files .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/REQUIREMENTS.md
 else
-  gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md .planning/REQUIREMENTS.md
+  gsd-sdk query commit "docs({phase}-{plan}): complete [plan-name] plan" --files .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md .planning/REQUIREMENTS.md
 fi
 ```
 </step>
@@ -458,7 +458,7 @@ git diff --name-only ${FIRST_TASK}^..HEAD 2>/dev/null || true
 Update only structural changes: new src/ dir → STRUCTURE.md | deps → STACK.md | file pattern → CONVENTIONS.md | API client → INTEGRATIONS.md | config → STACK.md | renamed → update paths. Skip code-only/bugfix/content changes.
 
 ```bash
-gsd-sdk query commit "" .planning/codebase/*.md --amend
+gsd-sdk query commit "" --files .planning/codebase/*.md --amend
 ```
 </step>
 
diff --git a/get-shit-done/workflows/explore.md b/get-shit-done/workflows/explore.md
index 4138c3bf5e..0e1d19461c 100644
--- a/get-shit-done/workflows/explore.md
+++ b/get-shit-done/workflows/explore.md
@@ -115,7 +115,7 @@ For each selected output, write the file:
 
 Commit if `commit_docs` is enabled:
 ```bash
-gsd-sdk query commit "docs: capture exploration — {topic_slug}" {file_list}
+gsd-sdk query commit "docs: capture exploration — {topic_slug}" --files {file_list}
 ```
 
 ## Step 6: Close
diff --git a/get-shit-done/workflows/import.md b/get-shit-done/workflows/import.md
index 5de222c3ac..a6f99aa608 100644
--- a/get-shit-done/workflows/import.md
+++ b/get-shit-done/workflows/import.md
@@ -220,7 +220,7 @@ Update `.planning/STATE.md` if appropriate (e.g., increment total plan count).
 
 Commit the imported plan and updated files:
 ```bash
-gsd-sdk query commit "docs({phase}): import plan from {basename FILEPATH}" .planning/phases/{phase}/{plan}-PLAN.md .planning/ROADMAP.md
+gsd-sdk query commit "docs({phase}): import plan from {basename FILEPATH}" --files .planning/phases/{phase}/{plan}-PLAN.md .planning/ROADMAP.md
 ```
 
 Display completion:
diff --git a/get-shit-done/workflows/ingest-docs.md b/get-shit-done/workflows/ingest-docs.md
index 24a52b3836..2273ba4ef5 100644
--- a/get-shit-done/workflows/ingest-docs.md
+++ b/get-shit-done/workflows/ingest-docs.md
@@ -289,7 +289,7 @@ Preview the merge diff to the user and gate via approve-revise-abort before writ
 Commit the ingest results:
 
 ```bash
-gsd-sdk query commit "docs: ingest {N} docs from {SCAN_PATH} (#2387)" \
+gsd-sdk query commit "docs: ingest {N} docs from {SCAN_PATH} (#2387)" --files \
   .planning/PROJECT.md \
   .planning/REQUIREMENTS.md \
   .planning/ROADMAP.md \
diff --git a/get-shit-done/workflows/map-codebase.md b/get-shit-done/workflows/map-codebase.md
index 40106db29f..ca1fa8b9bb 100644
--- a/get-shit-done/workflows/map-codebase.md
+++ b/get-shit-done/workflows/map-codebase.md
@@ -378,7 +378,7 @@ Continue to commit_codebase_map.
 Commit the codebase map:
 
 ```bash
-gsd-sdk query commit "docs: map existing codebase" .planning/codebase/*.md
+gsd-sdk query commit "docs: map existing codebase" --files .planning/codebase/*.md
 ```
 
 Continue to offer_next.
diff --git a/get-shit-done/workflows/milestone-summary.md b/get-shit-done/workflows/milestone-summary.md
index ea660a4d39..7d15ff56aa 100644
--- a/get-shit-done/workflows/milestone-summary.md
+++ b/get-shit-done/workflows/milestone-summary.md
@@ -189,7 +189,7 @@ mkdir -p .planning/reports
 
 Write the summary, then commit:
 ```bash
-gsd-sdk query commit "docs(v${VERSION}): generate milestone summary for onboarding" \
+gsd-sdk query commit "docs(v${VERSION}): generate milestone summary for onboarding" --files \
   ".planning/reports/MILESTONE_SUMMARY-v${VERSION}.md"
 ```
 
diff --git a/get-shit-done/workflows/new-milestone.md b/get-shit-done/workflows/new-milestone.md
index 15f54032cb..2bc54825eb 100644
--- a/get-shit-done/workflows/new-milestone.md
+++ b/get-shit-done/workflows/new-milestone.md
@@ -212,7 +212,7 @@ gsd-sdk query phases.clear --confirm
 ```
 
 ```bash
-gsd-sdk query commit "docs: start milestone v[X.Y] [Name]" .planning/PROJECT.md .planning/STATE.md
+gsd-sdk query commit "docs: start milestone v[X.Y] [Name]" --files .planning/PROJECT.md .planning/STATE.md
 ```
 
 ## 7. Load Context and Resolve Models
@@ -444,7 +444,7 @@ If "adjust": Return to scoping.
 
 **Commit requirements:**
 ```bash
-gsd-sdk query commit "docs: define milestone v[X.Y] requirements" .planning/REQUIREMENTS.md
+gsd-sdk query commit "docs: define milestone v[X.Y] requirements" --files .planning/REQUIREMENTS.md
 ```
 
 ## 10. Create Roadmap
@@ -530,7 +530,7 @@ Success criteria:
 
 **Commit roadmap** (after approval):
 ```bash
-gsd-sdk query commit "docs: create milestone v[X.Y] roadmap ([N] phases)" .planning/ROADMAP.md .planning/STATE.md .planning/REQUIREMENTS.md
+gsd-sdk query commit "docs: create milestone v[X.Y] roadmap ([N] phases)" --files .planning/ROADMAP.md .planning/STATE.md .planning/REQUIREMENTS.md
 ```
 
 ## 10.5. Link Pending Todos to Roadmap Phases
@@ -573,7 +573,7 @@ files: [existing]
 
 **If any todos were linked:**
 ```bash
-gsd-sdk query commit "docs: tag [count] pending todos with resolves_phase after milestone v[X.Y] roadmap" .planning/todos/pending/*.md
+gsd-sdk query commit "docs: tag [count] pending todos with resolves_phase after milestone v[X.Y] roadmap" --files .planning/todos/pending/*.md
 ```
 
 Print a summary:
diff --git a/get-shit-done/workflows/new-project.md b/get-shit-done/workflows/new-project.md
index fb4131ef6f..cbf3a4096e 100644
--- a/get-shit-done/workflows/new-project.md
+++ b/get-shit-done/workflows/new-project.md
@@ -236,7 +236,7 @@ gsd-sdk query config-new-project '{"mode":"yolo","granularity":"[selected]","par
 
 ```bash
 mkdir -p .planning
-gsd-sdk query commit "chore: add project config" .planning/config.json
+gsd-sdk query commit "chore: add project config" --files .planning/config.json
 ```
 
 **Persist auto-advance chain flag to config (survives context compaction):**
@@ -447,7 +447,7 @@ Do not compress. Capture everything gathered.
 
 ```bash
 mkdir -p .planning
-gsd-sdk query commit "docs: initialize project" .planning/PROJECT.md
+gsd-sdk query commit "docs: initialize project" --files .planning/PROJECT.md
 ```
 
 ## 5. Workflow Preferences
@@ -666,7 +666,7 @@ gsd-sdk query config-new-project '{"mode":"[yolo|interactive]","granularity":"[s
 **Commit config.json:**
 
 ```bash
-gsd-sdk query commit "chore: add project config" .planning/config.json
+gsd-sdk query commit "chore: add project config" --files .planning/config.json
 ```
 
 ## 5.1. Sub-Repo Detection
@@ -1114,7 +1114,7 @@ If "adjust": Return to scoping.
 **Commit requirements:**
 
 ```bash
-gsd-sdk query commit "docs: define v1 requirements" .planning/REQUIREMENTS.md
+gsd-sdk query commit "docs: define v1 requirements" --files .planning/REQUIREMENTS.md
 ```
 
 ## 8. Create Roadmap
@@ -1266,7 +1266,7 @@ This ensures new projects get the default GSD workflow-enforcement guidance and
 **Commit roadmap (after approval or auto mode):**
 
 ```bash
-gsd-sdk query commit "docs: create roadmap ([N] phases)" .planning/ROADMAP.md .planning/STATE.md .planning/REQUIREMENTS.md "$INSTRUCTION_FILE"
+gsd-sdk query commit "docs: create roadmap ([N] phases)" --files .planning/ROADMAP.md .planning/STATE.md .planning/REQUIREMENTS.md "$INSTRUCTION_FILE"
 ```
 
 ## 9. Done
diff --git a/get-shit-done/workflows/pause-work.md b/get-shit-done/workflows/pause-work.md
index f4bb5c7d99..7d7dec9945 100644
--- a/get-shit-done/workflows/pause-work.md
+++ b/get-shit-done/workflows/pause-work.md
@@ -207,7 +207,7 @@ timestamp=$(gsd-sdk query current-timestamp full --raw)
 
 <step name="commit">
 ```bash
-gsd-sdk query commit "wip: [context-name] paused at [X]/[Y]" [handoff-path] .planning/HANDOFF.json
+gsd-sdk query commit "wip: [context-name] paused at [X]/[Y]" --files [handoff-path] .planning/HANDOFF.json
 ```
 </step>
 
diff --git a/get-shit-done/workflows/plan-milestone-gaps.md b/get-shit-done/workflows/plan-milestone-gaps.md
index b87feb8d6e..7f05c2f078 100644
--- a/get-shit-done/workflows/plan-milestone-gaps.md
+++ b/get-shit-done/workflows/plan-milestone-gaps.md
@@ -146,7 +146,7 @@ mkdir -p ".planning/phases/{NN}-{name}"
 ## 9. Commit Roadmap and Requirements Update
 
 ```bash
-gsd-sdk query commit "docs(roadmap): add gap closure phases {N}-{M}" .planning/ROADMAP.md .planning/REQUIREMENTS.md
+gsd-sdk query commit "docs(roadmap): add gap closure phases {N}-{M}" --files .planning/ROADMAP.md .planning/REQUIREMENTS.md
 ```
 
 ## 10. Offer Next Steps
diff --git a/get-shit-done/workflows/plan-phase.md b/get-shit-done/workflows/plan-phase.md
index 06f8b6e23e..88efcc982f 100644
--- a/get-shit-done/workflows/plan-phase.md
+++ b/get-shit-done/workflows/plan-phase.md
@@ -201,7 +201,7 @@ Use full relative paths. Group by topic area.]
 
 5. Commit:
 ```bash
-gsd-sdk query commit "docs(${padded_phase}): generate context from PRD" "${phase_dir}/${padded_phase}-CONTEXT.md"
+gsd-sdk query commit "docs(${padded_phase}): generate context from PRD" --files "${phase_dir}/${padded_phase}-CONTEXT.md"
 ```
 
 6. Set `context_content` to the generated CONTEXT.md content and continue to step 5 (Handle Research).
@@ -925,7 +925,7 @@ For each plan entry extracted from `PLAN-OUTLINE.md`:
 
 5. **Commit per-plan:**
    ```bash
-   gsd-sdk query commit "docs(${PADDED_PHASE}): plan ${plan_id} (chunked)" "${PHASE_DIR}/${plan_id}-PLAN.md"
+   gsd-sdk query commit "docs(${PADDED_PHASE}): plan ${plan_id} (chunked)" --files "${PHASE_DIR}/${plan_id}-PLAN.md"
    ```
 
 After all N plans are written and committed, treat this as `## PLANNING COMPLETE` and continue
@@ -1263,7 +1263,7 @@ After the script returns, check that the bounced file still has valid YAML front
 
 6. **Commit surviving bounced plans:** If at least one plan survived both the frontmatter validation and the checker re-run, commit the changes:
 ```bash
-gsd-sdk query commit "refactor(${padded_phase}): bounce plans through external refinement" "${PHASE_DIR}/*-PLAN.md"
+gsd-sdk query commit "refactor(${padded_phase}): bounce plans through external refinement" --files "${PHASE_DIR}/*-PLAN.md"
 ```
 
 Display summary:
diff --git a/get-shit-done/workflows/plant-seed.md b/get-shit-done/workflows/plant-seed.md
index 85c463f3dd..41e5850d6a 100644
--- a/get-shit-done/workflows/plant-seed.md
+++ b/get-shit-done/workflows/plant-seed.md
@@ -143,7 +143,7 @@ Related code and decisions found in the current codebase:
 
 <step name="commit_seed">
 ```bash
-gsd-sdk query commit "docs: plant seed — {$IDEA}" .planning/seeds/SEED-{PADDED}-{slug}.md
+gsd-sdk query commit "docs: plant seed — {$IDEA}" --files .planning/seeds/SEED-{PADDED}-{slug}.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/quick.md b/get-shit-done/workflows/quick.md
index 054b005ef3..bb4301e16e 100644
--- a/get-shit-done/workflows/quick.md
+++ b/get-shit-done/workflows/quick.md
@@ -919,7 +919,7 @@ if [ "$COMMIT_DOCS" = "false" ]; then
 else
   git add ${file_list} 2>/dev/null
 fi
-gsd-sdk query commit "docs(quick-${quick_id}): ${DESCRIPTION}" ${file_list}
+gsd-sdk query commit "docs(quick-${quick_id}): ${DESCRIPTION}" --files ${file_list}
 ```
 
 Get final commit hash:
diff --git a/get-shit-done/workflows/remove-phase.md b/get-shit-done/workflows/remove-phase.md
index 0da8041422..645c115502 100644
--- a/get-shit-done/workflows/remove-phase.md
+++ b/get-shit-done/workflows/remove-phase.md
@@ -103,7 +103,7 @@ Extract from result: `removed`, `directory_deleted`, `renamed_directories`, `ren
 Stage and commit the removal:
 
 ```bash
-gsd-sdk query commit "chore: remove phase {target} ({original-phase-name})" .planning/
+gsd-sdk query commit "chore: remove phase {target} ({original-phase-name})" --files .planning/
 ```
 
 The commit message preserves the historical record of what was removed.
diff --git a/get-shit-done/workflows/review.md b/get-shit-done/workflows/review.md
index 7071e9144d..8284055827 100644
--- a/get-shit-done/workflows/review.md
+++ b/get-shit-done/workflows/review.md
@@ -410,7 +410,7 @@ plans_reviewed: [{list of PLAN.md files}]
 
 Commit:
 ```bash
-gsd-sdk query commit "docs: cross-AI review for phase {N}" {phase_dir}/{padded_phase}-REVIEWS.md
+gsd-sdk query commit "docs: cross-AI review for phase {N}" --files {phase_dir}/{padded_phase}-REVIEWS.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/ship.md b/get-shit-done/workflows/ship.md
index 947c64cec4..5cc276df67 100644
--- a/get-shit-done/workflows/ship.md
+++ b/get-shit-done/workflows/ship.md
@@ -257,7 +257,7 @@ gsd-sdk query state.update "Status" "Phase ${PHASE_NUMBER} shipped — PR #${PR_
 
 If `commit_docs` is true:
 ```bash
-gsd-sdk query commit "docs(${padded_phase}): ship phase ${PHASE_NUMBER} — PR #${PR_NUMBER}" .planning/STATE.md
+gsd-sdk query commit "docs(${padded_phase}): ship phase ${PHASE_NUMBER} — PR #${PR_NUMBER}" --files .planning/STATE.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/sketch-wrap-up.md b/get-shit-done/workflows/sketch-wrap-up.md
index 6ae4bbf7b4..6edf9d39a1 100644
--- a/get-shit-done/workflows/sketch-wrap-up.md
+++ b/get-shit-done/workflows/sketch-wrap-up.md
@@ -232,7 +232,7 @@ If this routing line already exists (append mode), leave it as-is.
 Commit all artifacts (if `COMMIT_DOCS` is true):
 
 ```bash
-gsd-sdk query commit "docs(sketch-wrap-up): package [N] sketch findings into project skill" .planning/sketches/WRAP-UP-SUMMARY.md
+gsd-sdk query commit "docs(sketch-wrap-up): package [N] sketch findings into project skill" --files .planning/sketches/WRAP-UP-SUMMARY.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/sketch.md b/get-shit-done/workflows/sketch.md
index 335d693620..151b5433e6 100644
--- a/get-shit-done/workflows/sketch.md
+++ b/get-shit-done/workflows/sketch.md
@@ -296,7 +296,7 @@ Iterate until satisfied.
 
 **h.** Commit (if `COMMIT_DOCS` is true):
 ```bash
-gsd-sdk query commit "docs(sketch-NNN): [winning direction] — [key visual insight]" .planning/sketches/NNN-descriptive-name/ .planning/sketches/MANIFEST.md
+gsd-sdk query commit "docs(sketch-NNN): [winning direction] — [key visual insight]" --files .planning/sketches/NNN-descriptive-name/ .planning/sketches/MANIFEST.md
 ```
 
 **i.** Report:
diff --git a/get-shit-done/workflows/spike-wrap-up.md b/get-shit-done/workflows/spike-wrap-up.md
index 46c03aeb84..fd72b4d02d 100644
--- a/get-shit-done/workflows/spike-wrap-up.md
+++ b/get-shit-done/workflows/spike-wrap-up.md
@@ -246,7 +246,7 @@ Patterns and stack choices established across spike sessions. New spikes follow
 Commit all artifacts (if `COMMIT_DOCS` is true):
 
 ```bash
-gsd-sdk query commit "docs(spike-wrap-up): package [N] spike findings into project skill" .planning/spikes/WRAP-UP-SUMMARY.md .planning/spikes/CONVENTIONS.md
+gsd-sdk query commit "docs(spike-wrap-up): package [N] spike findings into project skill" --files .planning/spikes/WRAP-UP-SUMMARY.md .planning/spikes/CONVENTIONS.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/spike.md b/get-shit-done/workflows/spike.md
index 7204b1a2a6..a91677966e 100644
--- a/get-shit-done/workflows/spike.md
+++ b/get-shit-done/workflows/spike.md
@@ -334,7 +334,7 @@ tags: [tag1, tag2]
 
 **i.** Commit (if `COMMIT_DOCS` is true):
 ```bash
-gsd-sdk query commit "docs(spike-NNN): [VERDICT] — [key finding]" .planning/spikes/NNN-descriptive-name/ .planning/spikes/MANIFEST.md
+gsd-sdk query commit "docs(spike-NNN): [VERDICT] — [key finding]" --files .planning/spikes/NNN-descriptive-name/ .planning/spikes/MANIFEST.md
 ```
 
 **j.** Report:
@@ -388,7 +388,7 @@ Only include patterns that repeated across 2+ spikes or were explicitly chosen b
 
 Commit (if `COMMIT_DOCS` is true):
 ```bash
-gsd-sdk query commit "docs(spikes): update conventions" .planning/spikes/CONVENTIONS.md
+gsd-sdk query commit "docs(spikes): update conventions" --files .planning/spikes/CONVENTIONS.md
 ```
 </step>
 
diff --git a/get-shit-done/workflows/ui-phase.md b/get-shit-done/workflows/ui-phase.md
index dfbf5c3c3e..c404e1aa70 100644
--- a/get-shit-done/workflows/ui-phase.md
+++ b/get-shit-done/workflows/ui-phase.md
@@ -298,7 +298,7 @@ Dimensions: 6/6 passed
 ## 11. Commit (if configured)
 
 ```bash
-gsd-sdk query commit "docs(${padded_phase}): UI design contract" "${PHASE_DIR}/${PADDED_PHASE}-UI-SPEC.md"
+gsd-sdk query commit "docs(${padded_phase}): UI design contract" --files "${PHASE_DIR}/${PADDED_PHASE}-UI-SPEC.md"
 ```
 
 ## 12. Update State
diff --git a/get-shit-done/workflows/ui-review.md b/get-shit-done/workflows/ui-review.md
index bb3e529c38..31bdab71fd 100644
--- a/get-shit-done/workflows/ui-review.md
+++ b/get-shit-done/workflows/ui-review.md
@@ -176,7 +176,7 @@ tools is detected at runtime.
 ## 5. Commit (if configured)
 
 ```bash
-gsd-sdk query commit "docs(${padded_phase}): UI audit review" "${PHASE_DIR}/${PADDED_PHASE}-UI-REVIEW.md"
+gsd-sdk query commit "docs(${padded_phase}): UI audit review" --files "${PHASE_DIR}/${PADDED_PHASE}-UI-REVIEW.md"
 ```
 
 </process>
diff --git a/get-shit-done/workflows/verify-work.md b/get-shit-done/workflows/verify-work.md
index 76cf4b398b..26812ca12f 100644
--- a/get-shit-done/workflows/verify-work.md
+++ b/get-shit-done/workflows/verify-work.md
@@ -391,7 +391,7 @@ Clear Current Test section:
 
 Commit the UAT file:
 ```bash
-gsd-sdk query commit "test({phase_num}): complete UAT - {passed} passed, {issues} issues" ".planning/phases/XX-name/{phase_num}-UAT.md"
+gsd-sdk query commit "test({phase_num}): complete UAT - {passed} passed, {issues} issues" --files ".planning/phases/XX-name/{phase_num}-UAT.md"
 ```
 
 Present summary:
diff --git a/tests/bug-2767-gsd-sdk-commit-files-flag.test.cjs b/tests/bug-2767-gsd-sdk-commit-files-flag.test.cjs
new file mode 100644
index 0000000000..81707fd5fd
--- /dev/null
+++ b/tests/bug-2767-gsd-sdk-commit-files-flag.test.cjs
@@ -0,0 +1,302 @@
+/**
+ * Bug #2767: Workflows pass paths positionally to `gsd-sdk query commit`.
+ *
+ * Runtime behavior under the buggy form (paths positional, no `--files`):
+ *   1. positional path tokens are joined into the commit subject (commit.ts:110); and
+ *   2. `filePaths` is empty, so the handler falls back to staging `.planning/`
+ *      wholesale (commit.ts:136), silently swapping the user's intent.
+ *
+ * Under the well-formed form (`--files <path...>`):
+ *   - subject is the message arg only;
+ *   - exactly the listed files are staged;
+ *   - `commit-to-subrepo` rejects when `--files` is absent (commit.ts:258).
+ *
+ * Note: the supplementary doc-lint's `isWellFormed` accepts any invocation that
+ * has no positional path args after the message — i.e. message-only commits pass
+ * regardless of any trailing comment. There is no required marker (`# message-only`
+ * or otherwise); the absence of positional path tokens is the sole signal.
+ *
+ * Primary test: invoke the actual `gsd-sdk query commit[-to-subrepo]` binary
+ * against a real tmp git project and assert the runtime behavior. Supplementary
+ * test: a doc-lint that scans every shipped .md file to catch regressions of
+ * the 50-file invocation cleanup landed in this PR. The behavioral tests are
+ * the contract; the lint is a defense-in-depth guard.
+ */
+
+const { describe, test, beforeEach, afterEach } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
+const { execFileSync } = require('node:child_process');
+const { createTempGitProject, cleanup } = require('./helpers.cjs');
+
+const REPO_ROOT = path.join(__dirname, '..');
+const SDK_CLI = path.join(REPO_ROOT, 'sdk', 'dist', 'cli.js');
+
+/**
+ * Run a git command with hardcoded argv (no shell). Returns trimmed stdout.
+ */
+function git(projectDir, args) {
+  return execFileSync('git', args, { cwd: projectDir, encoding: 'utf-8' }).trim();
+}
+
+/**
+ * Invoke `gsd-sdk query <subcommand> <...args>` against a project dir.
+ * Returns { exitCode, stdout, stderr, json } where json is the parsed handler
+ * payload (the SDK prints a single JSON object to stdout for query handlers).
+ */
+function runSdkQuery(subcommand, args, projectDir) {
+  const argv = ['query', subcommand, ...args, '--project-dir', projectDir];
+  let stdout = '';
+  let stderr = '';
+  let exitCode = 0;
+  try {
+    stdout = execFileSync(process.execPath, [SDK_CLI, ...argv], {
+      encoding: 'utf-8',
+      stdio: ['pipe', 'pipe', 'pipe'],
+      env: { ...process.env, GSD_SESSION_KEY: '' },
+    });
+  } catch (err) {
+    exitCode = err.status ?? 1;
+    stdout = err.stdout?.toString() ?? '';
+    stderr = err.stderr?.toString() ?? '';
+  }
+  // Extract the trailing JSON object — the CLI prints status lines before it.
+  let json = null;
+  const lastBrace = stdout.lastIndexOf('{');
+  if (lastBrace >= 0) {
+    try { json = JSON.parse(stdout.slice(lastBrace).trim()); } catch { /* leave null */ }
+    if (!json) {
+      try { json = JSON.parse(stdout.trim()); } catch { /* leave null */ }
+    }
+  }
+  return { exitCode, stdout, stderr, json };
+}
+
+function gitSubject(projectDir) {
+  return git(projectDir, ['log', '-1', '--pretty=%s']);
+}
+
+function gitFilesAt(projectDir) {
+  return git(projectDir, ['show', '--pretty=', '--name-only', 'HEAD'])
+    .split('\n').filter(Boolean).sort();
+}
+
+// ─── Behavioral SDK tests ────────────────────────────────────────────────────
+
+describe('bug #2767 (behavioral): gsd-sdk query commit --files', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempGitProject('gsd-2767-');
+    fs.writeFileSync(path.join(tmpDir, 'foo.md'), 'foo body\n');
+    fs.writeFileSync(path.join(tmpDir, 'bar.md'), 'bar body\n');
+    // .planning/ change that MUST NOT leak into the commit when --files is used.
+    fs.writeFileSync(path.join(tmpDir, '.planning', 'STATE.md'), 'state\n');
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('well-formed: --files <paths> stages exactly those files with clean subject', () => {
+    const message = 'test(#2767): well-formed commit';
+    const result = runSdkQuery('commit', [message, '--files', 'foo.md', 'bar.md'], tmpDir);
+
+    assert.equal(result.exitCode, 0, `cli failed: ${result.stderr}`);
+    assert.ok(result.json, `expected JSON body in stdout, got:\n${result.stdout}`);
+    assert.equal(result.json.committed, true, `commit failed: ${JSON.stringify(result.json)}`);
+    assert.equal(result.json.message, message, 'subject must be message-only — no path leakage');
+    assert.deepEqual(result.json.files.slice().sort(), ['bar.md', 'foo.md']);
+
+    // Cross-check via git itself.
+    assert.equal(gitSubject(tmpDir), message);
+    assert.deepEqual(gitFilesAt(tmpDir), ['bar.md', 'foo.md']);
+    // The .planning/STATE.md change must remain unstaged/unrelated.
+    const stillDirty = git(tmpDir, ['status', '--porcelain']);
+    assert.ok(stillDirty.includes('.planning/STATE.md'),
+      `.planning/STATE.md should remain unstaged, got status:\n${stillDirty}`);
+  });
+
+  test('buggy form (positional, no --files): paths leak into subject AND .planning/ fallback fires', () => {
+    // Documents the misbehavior #2767 prevents at every workflow call site.
+    // Any future change that makes the buggy form silently "do the right thing"
+    // trips this test and must justify the change.
+    const message = 'test(#2767): positional buggy';
+    const result = runSdkQuery('commit', [message, 'foo.md', 'bar.md'], tmpDir);
+
+    assert.equal(result.exitCode, 0);
+    assert.ok(result.json, `expected JSON body, got:\n${result.stdout}`);
+    assert.equal(result.json.committed, true);
+
+    // Subject got polluted with the path tokens.
+    assert.equal(result.json.message, `${message} foo.md bar.md`,
+      'paths leak into the commit subject under the buggy form (commit.ts:110)');
+    assert.equal(gitSubject(tmpDir), `${message} foo.md bar.md`);
+
+    // Fallback staged .planning/STATE.md, NOT foo.md/bar.md.
+    assert.deepEqual(gitFilesAt(tmpDir), ['.planning/STATE.md'],
+      'positional form triggers the .planning/ wholesale fallback (commit.ts:136)');
+    const dirty = git(tmpDir, ['status', '--porcelain']);
+    assert.ok(dirty.includes('foo.md') && dirty.includes('bar.md'),
+      `foo.md/bar.md should remain unstaged under the buggy form, got:\n${dirty}`);
+  });
+
+  test('positional form with no .planning/ change: returns "nothing staged"', () => {
+    // Reset the .planning/STATE.md change so the fallback has nothing to stage.
+    fs.rmSync(path.join(tmpDir, '.planning', 'STATE.md'), { force: true });
+
+    const result = runSdkQuery('commit', ['msg', 'foo.md'], tmpDir);
+    assert.equal(result.exitCode, 0);
+    assert.ok(result.json, `expected JSON body, got:\n${result.stdout}`);
+    assert.equal(result.json.committed, false);
+    assert.equal(result.json.reason, 'nothing staged',
+      'positional form ignores foo.md and finds nothing under .planning/ to fall back to');
+  });
+});
+
+describe('bug #2767 (behavioral): commit-to-subrepo requires --files', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempGitProject('gsd-2767-sub-');
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ sub_repos: ['vendor/lib'] }, null, 2),
+    );
+    fs.mkdirSync(path.join(tmpDir, 'vendor', 'lib'), { recursive: true });
+    fs.writeFileSync(path.join(tmpDir, 'vendor', 'lib', 'README.md'), 'sub\n');
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('rejects with explicit error when --files is omitted', () => {
+    const result = runSdkQuery('commit-to-subrepo', ['only message, no files'], tmpDir);
+    assert.equal(result.exitCode, 0);
+    assert.ok(result.json, `expected JSON body, got:\n${result.stdout}`);
+    assert.equal(result.json.committed, false);
+    assert.equal(result.json.reason, '--files required for commit-to-subrepo',
+      'commit-to-subrepo enforces --files at runtime (commit.ts:258)');
+  });
+});
+
+// ─── Supplementary doc-lint (defense-in-depth) ───────────────────────────────
+//
+// The behavioral tests above prove the SDK semantics. This lint scans every
+// shipped .md invocation to catch regressions in the 50-file workflow cleanup
+// landed by this PR — without it, a future contributor adding a new workflow
+// could reintroduce the positional form silently. allow-test-rule: doc-text
+// invocations cannot be exercised end-to-end (they are agent-prompt strings
+// rendered into chat, not invoked by gsd-tools.cjs), so a textual guard is
+// the only available enforcement layer.
+
+const SCAN_DIRS = ['agents', 'commands', 'get-shit-done', 'docs', 'scripts'];
+const KNOWN_FLAGS = new Set(['--force', '--amend', '--no-verify', '--files']);
+
+function walk(dir, out = []) {
+  if (!fs.existsSync(dir)) return out;
+  for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+    const full = path.join(dir, entry.name);
+    if (entry.isDirectory()) {
+      if (entry.name === 'node_modules' || entry.name.startsWith('.')) continue;
+      walk(full, out);
+    } else if (entry.isFile() && entry.name.endsWith('.md')) {
+      out.push(full);
+    }
+  }
+  return out;
+}
+
+function extractInvocations(filePath) {
+  const text = fs.readFileSync(filePath, 'utf-8');
+  const lines = text.split(/\r?\n/);
+  const invocations = [];
+  for (let i = 0; i < lines.length; i++) {
+    const m = lines[i].match(/(gsd-sdk\s+query\s+commit(?:-to-subrepo)?\b.*)$/);
+    if (!m) continue;
+    const tail = m[1].match(/^gsd-sdk\s+query\s+commit(?:-to-subrepo)?(.?)/);
+    if (tail && tail[1] === '`') continue;
+    let cmd = m[1];
+    let j = i;
+    while (cmd.endsWith('\\') && j + 1 < lines.length) {
+      cmd = cmd.slice(0, -1).trimEnd() + ' ' + lines[j + 1].trim();
+      j++;
+    }
+    invocations.push({ line: i + 1, cmd, file: filePath });
+  }
+  return invocations;
+}
+
+function stripTail(cmd) {
+  let inSingle = false, inDouble = false;
+  for (let i = 0; i < cmd.length; i++) {
+    const c = cmd[i];
+    if (c === "'" && !inDouble) inSingle = !inSingle;
+    else if (c === '"' && !inSingle) inDouble = !inDouble;
+    else if (!inSingle && !inDouble) {
+      if (c === '#' && (i === 0 || /\s/.test(cmd[i - 1]))) return cmd.slice(0, i);
+      if (c === '|' || c === ';' || c === '>' || c === '<') return cmd.slice(0, i);
+      if (c === '&' && cmd[i + 1] === '&') return cmd.slice(0, i);
+    }
+  }
+  return cmd;
+}
+
+function tokenize(cmd) {
+  const out = [];
+  let cur = '', inSingle = false, inDouble = false;
+  for (let i = 0; i < cmd.length; i++) {
+    const c = cmd[i];
+    if (c === "'" && !inDouble) { inSingle = !inSingle; cur += c; continue; }
+    if (c === '"' && !inSingle) { inDouble = !inDouble; cur += c; continue; }
+    if (/\s/.test(c) && !inSingle && !inDouble) {
+      if (cur) { out.push(cur); cur = ''; }
+      continue;
+    }
+    cur += c;
+  }
+  if (cur) out.push(cur);
+  return out;
+}
+
+function isWellFormed(cmd) {
+  const truncated = stripTail(cmd);
+  const parts = tokenize(truncated);
+  if (parts.length < 3) return true;
+  const args = parts.slice(3);
+  if (args.length === 0) return true;
+  if (args.includes('--files')) return true;
+  let sawMessage = false;
+  for (const tok of args) {
+    if (KNOWN_FLAGS.has(tok)) continue;
+    if (!sawMessage) { sawMessage = true; continue; }
+    return false;
+  }
+  return true;
+}
+
+describe('bug #2767 (supplementary doc-lint): no positional invocations in shipped .md', () => {
+  const allFiles = SCAN_DIRS.flatMap(d => walk(path.join(REPO_ROOT, d)));
+  const allInvocations = allFiles.flatMap(extractInvocations);
+
+  test('lint scanned at least one invocation (sanity)', () => {
+    assert.ok(allInvocations.length > 0, 'lint scanned 0 invocations — globs are wrong');
+  });
+
+  test('every gsd-sdk query commit invocation either uses --files or has no path args', () => {
+    const broken = allInvocations.filter(({ cmd }) => !isWellFormed(cmd));
+    if (broken.length > 0) {
+      const detail = broken.map(({ file, line, cmd }) => {
+        const rel = path.relative(REPO_ROOT, file);
+        return `  ${rel}:${line}\n    ${cmd}`;
+      }).join('\n');
+      assert.fail(
+        `${broken.length} \`gsd-sdk query commit\` invocation(s) pass paths positionally.\n` +
+        `The behavioral test above proves what goes wrong at runtime; this lint catches\n` +
+        `regressions in shipped workflow markdown.\n${detail}`
+      );
+    }
+  });
+});