chore: cherry-pick upstream Tier 2 workflow engine (11 commits) — batch 3

.archon/commands/defaults/archon-create-pr.md

@@ -84,8 +84,17 @@ git status --porcelain
 ```
 
 **If dirty**:
-1. Stage changes: `git add -A`
-2. Commit: `git commit -m "Final changes before PR"`
+
+1. Stage **only** the source files that are part of this change — never `git add -A`, `git add .`, or `git add -u`. List them by name:
+   ```bash
+   git add path/to/file1 path/to/file2 ...
+   git status --porcelain  # verify nothing else is staged
+   ```
+2. **Never stage** scratch / review / PR-body artifacts, even if they show up in `git status`:
+   - `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`
+   - `review/`, `*-report.md` at the repo root
+   - Anything under `$ARTIFACTS_DIR`
+3. Commit: `git commit -m "Final changes before PR"`
 
 ### 2.2 Push Branch
 

.archon/commands/defaults/archon-finalize-pr.md

@@ -71,13 +71,20 @@ git status --porcelain
 
 ### 2.2 Stage Changes
 
-Stage all implementation changes:
+Stage **only** the implementation files you actually edited — never `git add -A`, `git add .`, or `git add -u`. List them by name:
 
 ```bash
-git add -A
+git add path/to/file1 path/to/file2 ...
+git status --porcelain  # verify nothing else is staged
 ```
 
-**Review staged files** - ensure no sensitive files (.env, credentials) are included:
+**Never stage** scratch / review / PR-body artifacts, even if they appear in `git status`:
+
+- `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`
+- `review/`, `*-report.md` at the repo root
+- Anything under `$ARTIFACTS_DIR`
+
+**Review staged files** — ensure no sensitive files (`.env`, credentials) and no scratch artifacts are included:
 
 ```bash
 git diff --cached --name-only

.archon/commands/defaults/archon-fix-issue.md

@@ -294,11 +294,19 @@ Execute any manual verification steps from the artifact.
 
 ### 7.1 Stage Changes
 
+Stage **only** the files you actually edited — never `git add -A`, `git add .`, or `git add -u`. List them by name:
+
 ```bash
-git add -A
-git status  # Review what's being committed
+git add path/to/file1 path/to/file2 ...
+git status --porcelain  # verify nothing scratch/review/PR-body is staged
 ```
 
+**Never stage**:
+
+- `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`
+- `review/`, `*-report.md` at the repo root
+- Anything under `$ARTIFACTS_DIR`
+
 ### 7.2 Write Commit Message
 
 **Format:**

.archon/commands/defaults/archon-implement-issue.md

@@ -295,11 +295,19 @@ Execute any manual verification steps from the artifact.
 
 ### 7.1 Stage Changes
 
+Stage **only** the files you actually edited — never `git add -A`, `git add .`, or `git add -u`. List them by name:
+
 ```bash
-git add -A
-git status  # Review what's being committed
+git add path/to/file1 path/to/file2 ...
+git status --porcelain  # verify nothing scratch/review/PR-body is staged
 ```
 
+**Never stage**:
+
+- `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`
+- `review/`, `*-report.md` at the repo root
+- Anything under `$ARTIFACTS_DIR`
+
 ### 7.2 Write Commit Message
 
 **Format:**
@@ -367,7 +375,8 @@ Write the prepared body to `$ARTIFACTS_DIR/pr-body.md`, then:
 
 ```bash
 gh pr create --title "Fix: {title} (#{number})" \
-  --body-file $ARTIFACTS_DIR/pr-body.md
+  --body-file $ARTIFACTS_DIR/pr-body.md \
+  --base $BASE_BRANCH
 ```
 
 ### 8.3 Get PR Number

.archon/commands/defaults/archon-implement-review-fixes.md

@@ -175,11 +175,19 @@ Must succeed.
 
 ### 4.1 Stage Changes
 
+Stage **only** the files you actually edited while applying review fixes — never `git add -A`, `git add .`, or `git add -u`. List them by name:
+
 ```bash
-git add -A
-git status
+git add path/to/file1 path/to/file2 ...
+git status --porcelain  # verify nothing scratch/review/PR-body is staged
 ```
 
+**Never stage**:
+
+- `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`
+- `review/`, `*-report.md` at the repo root
+- Anything under `$ARTIFACTS_DIR` (review artifacts live here, not in the worktree)
+
 ### 4.2 Commit
 
 ```bash

.archon/commands/defaults/archon-simplify-changes.md

@@ -61,16 +61,29 @@ For each simplification:
 2. Run `bun run type-check` — if it fails, revert that change
 3. Run `bun run lint` — if it fails, fix or revert
 
+**Track every path you edit.** You will need this list in Phase 3 to stage only the files you touched.
+
 ### Phase 3: VALIDATE & COMMIT
 
 1. Run full validation: `bun run type-check && bun run lint`
-2. If changes were made:
+2. If simplifications were applied, stage **only** the files you edited in Phase 2 — never `git add -A`, `git add .`, or `git add -u`:
+   ```bash
+   # Stage by name, using the list you tracked in Phase 2
+   git add path/to/file1.ts path/to/file2.ts
+   # Verify nothing else snuck in
+   git status --porcelain
+   ```
+3. **Never stage** report, scratch, or PR-body artifacts, even if they show up as untracked or modified in the worktree:
+   - Anything under `$ARTIFACTS_DIR` (the artifacts directory normally lives outside the worktree, but copies/symlinks may exist)
+   - `review/`, `simplify-report.md`, `*-report.md` at the repo root
+   - `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`
+   - If `git status --porcelain` shows files you don't recognize as part of your simplifications, leave them unstaged
+4. Commit and push only the staged source edits:
    ```bash
-   git add -A
    git commit -m "simplify: reduce complexity in changed files"
    git push
    ```
-3. If no simplifications found, skip commit
+5. If no simplifications were applied, skip the commit entirely
 
 ### Phase 4: REPORT
 

.archon/workflows/defaults/archon-architect.yaml

@@ -312,7 +312,8 @@ nodes:
       1. Stage all changes and create a single commit (or verify existing commits)
       2. Push the branch: `git push -u origin HEAD`
       3. Check if a PR already exists: `gh pr list --head $(git branch --show-current)`
-      4. Create the PR with:
+      4. Create the PR targeting `$BASE_BRANCH` as the base branch:
+         `gh pr create --base $BASE_BRANCH --title "..." --body "..."`
          - Title: concise description of what was simplified (under 70 chars)
          - Body: use the format below
       5. Save the PR URL to `$ARTIFACTS_DIR/.pr-url`
@@ -357,3 +358,17 @@ nodes:
               additionalContext: >
                 Verify this command succeeded. If git push or gh pr create failed,
                 read the error message carefully before retrying.
+
+  - id: verify-pr-base
+    bash: |
+      set -euo pipefail
+      EXPECTED="$BASE_BRANCH"
+      ACTUAL=$(gh pr view --json baseRefName -q '.baseRefName')
+      if [ "$ACTUAL" != "$EXPECTED" ]; then
+        PR_NUMBER=$(gh pr view --json number -q '.number')
+        echo "Base mismatch on PR #$PR_NUMBER: expected=$EXPECTED actual=$ACTUAL — re-targeting" >&2
+        gh pr edit "$PR_NUMBER" --base "$EXPECTED"
+      else
+        echo "PR base verified: $EXPECTED"
+      fi
+    depends_on: [create-pr]

.archon/workflows/defaults/archon-feature-development.yaml

@@ -14,3 +14,17 @@ nodes:
     command: archon-create-pr
     depends_on: [implement]
     context: fresh
+
+  - id: verify-pr-base
+    bash: |
+      set -euo pipefail
+      EXPECTED="$BASE_BRANCH"
+      ACTUAL=$(gh pr view --json baseRefName -q '.baseRefName')
+      if [ "$ACTUAL" != "$EXPECTED" ]; then
+        PR_NUMBER=$(gh pr view --json number -q '.number')
+        echo "Base mismatch on PR #$PR_NUMBER: expected=$EXPECTED actual=$ACTUAL — re-targeting" >&2
+        gh pr edit "$PR_NUMBER" --base "$EXPECTED"
+      else
+        echo "PR base verified: $EXPECTED"
+      fi
+    depends_on: [create-pr]

.archon/workflows/defaults/archon-fix-github-issue.yaml

@@ -160,7 +160,14 @@ nodes:
 
       ## Instructions
 
-      1. Check git status — ensure all changes are committed. If uncommitted changes exist, stage and commit them.
+      1. Check git status. If uncommitted changes exist, stage and commit ONLY source files that are part of the fix:
+         - List them by name with `git add <path1> <path2> ...` — never `git add -A`, `git add .`, or `git add -u`
+         - **Never commit** scratch / review / PR-body artifacts, even if they appear in `git status`:
+           - `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md` at any path
+           - `review/`, `*-report.md` at the repo root
+           - Anything under `$ARTIFACTS_DIR`
+         - Verify with `git status --porcelain` that nothing scratch is staged before committing
+         - If files you don't recognize as part of the fix appear modified or untracked, leave them alone
       2. Push the branch: `git push -u origin HEAD`
       3. Read implementation artifacts from `$ARTIFACTS_DIR/` for context:
          - `$ARTIFACTS_DIR/investigation.md` or `$ARTIFACTS_DIR/plan.md`
@@ -172,6 +179,7 @@ nodes:
       6. Create a DRAFT PR: `gh pr create --draft --base $BASE_BRANCH`
          - Title: concise, imperative mood, under 70 chars
          - Body: if a PR template was found, fill in **every section** with details from the artifacts. Don't skip sections or leave placeholders. If no template, write a body with summary, changes, validation evidence, and `Fixes #...`.
+         - **PR body file location**: if you write the body to a file (e.g. for `--body-file`), the file MUST live at `$ARTIFACTS_DIR/pr-body.md` or under `/tmp/` — NEVER inside the worktree. Files like `.pr-body.md` at the repo root will be picked up by later commits.
          - Link to issue: include `Fixes #...` or `Closes #...`
       7. Capture PR identifiers:
          ```bash
@@ -187,9 +195,23 @@ nodes:
   # PHASE 7: REVIEW
   # ═══════════════════════════════════════════════════════════════
 
+  - id: verify-pr-base
+    bash: |
+      set -euo pipefail
+      EXPECTED="$BASE_BRANCH"
+      ACTUAL=$(gh pr view --json baseRefName -q '.baseRefName')
+      if [ "$ACTUAL" != "$EXPECTED" ]; then
+        PR_NUMBER=$(gh pr view --json number -q '.number')
+        echo "Base mismatch on PR #$PR_NUMBER: expected=$EXPECTED actual=$ACTUAL — re-targeting" >&2
+        gh pr edit "$PR_NUMBER" --base "$EXPECTED"
+      else
+        echo "PR base verified: $EXPECTED"
+      fi
+    depends_on: [create-pr]
+
   - id: review-scope
     command: archon-pr-review-scope
-    depends_on: [create-pr]
+    depends_on: [verify-pr-base]
     context: fresh
 
   - id: review-classify

.archon/workflows/defaults/archon-idea-to-pr.yaml

@@ -76,9 +76,23 @@ nodes:
   # PHASE 6: CODE REVIEW
   # ═══════════════════════════════════════════════════════════════════
 
+  - id: verify-pr-base
+    bash: |
+      set -euo pipefail
+      EXPECTED="$BASE_BRANCH"
+      ACTUAL=$(gh pr view --json baseRefName -q '.baseRefName')
+      if [ "$ACTUAL" != "$EXPECTED" ]; then
+        PR_NUMBER=$(gh pr view --json number -q '.number')
+        echo "Base mismatch on PR #$PR_NUMBER: expected=$EXPECTED actual=$ACTUAL — re-targeting" >&2
+        gh pr edit "$PR_NUMBER" --base "$EXPECTED"
+      else
+        echo "PR base verified: $EXPECTED"
+      fi
+    depends_on: [finalize-pr]
+
   - id: review-scope
     command: archon-pr-review-scope
-    depends_on: [finalize-pr]
+    depends_on: [verify-pr-base]
     context: fresh
 
   - id: sync

.archon/workflows/defaults/archon-issue-review-full.yaml

@@ -33,9 +33,23 @@ nodes:
   # PHASE 3: CODE REVIEW
   # ═══════════════════════════════════════════════════════════════════
 
+  - id: verify-pr-base
+    bash: |
+      set -euo pipefail
+      EXPECTED="$BASE_BRANCH"
+      ACTUAL=$(gh pr view --json baseRefName -q '.baseRefName')
+      if [ "$ACTUAL" != "$EXPECTED" ]; then
+        PR_NUMBER=$(gh pr view --json number -q '.number')
+        echo "Base mismatch on PR #$PR_NUMBER: expected=$EXPECTED actual=$ACTUAL — re-targeting" >&2
+        gh pr edit "$PR_NUMBER" --base "$EXPECTED"
+      else
+        echo "PR base verified: $EXPECTED"
+      fi
+    depends_on: [implement]
+
   - id: review-scope
     command: archon-pr-review-scope
-    depends_on: [implement]
+    depends_on: [verify-pr-base]
     context: fresh
 
   - id: sync

.archon/workflows/defaults/archon-piv-loop.yaml

@@ -500,8 +500,11 @@ nodes:
 
         ## Phase 4: COMMIT — Save Changes
 
+        Stage **only** the files you edited for this PIV task — never `git add -A`, `git add .`, or `git add -u`. List them by name:
+
         ```bash
-        git add -A
+        git add path/to/file1 path/to/file2 ...
+        git status --porcelain  # verify nothing scratch/review/PR-body is staged
         git diff --cached --stat
         git commit -m "$(cat <<'EOF'
         {type}: {task description}
@@ -511,7 +514,13 @@ nodes:
         )"
         ```
 
+<<<<<<< HEAD
         Track progress in `.claude/archon/plans/progress.txt`:
+=======
+        **Never stage**: `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`, `review/`, `*-report.md` at the repo root, or anything under `$ARTIFACTS_DIR`.
+
+        Track progress in `$ARTIFACTS_DIR/progress.txt`:
+>>>>>>> 8295ece7 (fix(workflows): stop sweeping scratch artifacts from every git add -A site (#1506))
         ```
         ## Task {N}: {title} — COMPLETED
         Date: {ISO date}
@@ -579,11 +588,19 @@ nodes:
 
       ## Step 5: Fix Obvious Issues
 
-      Fix type errors, lint warnings, missing imports, formatting. Commit any fixes:
+      Fix type errors, lint warnings, missing imports, formatting. Stage only the files you fixed — never `git add -A`. Skip the commit if there were no fixes:
       ```bash
+<<<<<<< HEAD
       git add -A && git commit -m "fix: address code review findings" 2>/dev/null || true
+=======
+      git add path/to/file1 path/to/file2 ...  # list real fixes only
+      git status --porcelain  # verify nothing scratch/review/PR-body is staged
+      git diff --cached --quiet || git commit -m "fix: address code review findings"
+>>>>>>> 8295ece7 (fix(workflows): stop sweeping scratch artifacts from every git add -A site (#1506))
       ```
 
+      **Never stage**: `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`, `review/`, `*-report.md` at the repo root, or anything under `$ARTIFACTS_DIR`.
+
       ## Step 6: Present Review
 
       ```
@@ -660,8 +677,11 @@ nodes:
 
         ## Step 4: Commit Fixes
 
+        Stage **only** the files you actually edited while addressing feedback — never `git add -A`. List them by name:
+
         ```bash
-        git add -A
+        git add path/to/file1 path/to/file2 ...
+        git status --porcelain  # verify nothing scratch/review/PR-body is staged
         git commit -m "$(cat <<'EOF'
         fix: address review feedback
 
@@ -672,6 +692,8 @@ nodes:
         )"
         ```
 
+        **Never stage**: `.pr-body.md`, `pr-body.md`, `*.scratch.md`, `*.tmp.md`, `review/`, `*-report.md` at the repo root, or anything under `$ARTIFACTS_DIR`.
+
         ## Step 5: Report
 
         ```
@@ -764,3 +786,17 @@ nodes:
       All checks passed.
       ===============================================================
       ```
+
+  - id: verify-pr-base
+    bash: |
+      set -euo pipefail
+      EXPECTED="$BASE_BRANCH"
+      ACTUAL=$(gh pr view --json baseRefName -q '.baseRefName')
+      if [ "$ACTUAL" != "$EXPECTED" ]; then
+        PR_NUMBER=$(gh pr view --json number -q '.number')
+        echo "Base mismatch on PR #$PR_NUMBER: expected=$EXPECTED actual=$ACTUAL — re-targeting" >&2
+        gh pr edit "$PR_NUMBER" --base "$EXPECTED"
+      else
+        echo "PR base verified: $EXPECTED"
+      fi
+    depends_on: [finalize]