Merge master into MovingBubblesFresh-clean

Resolve 12 file conflicts:
- Accept master's dead code cleanup (unused module-level vars, uncalled
  subroutines like s_compute_fd_divergence, s_solve_linear_system,
  s_convert_cylindrical_to_spherical_coord, flg, gm_alpha_qp, M11)
- Keep PR's intentional changes: max_dt refactor from 3D array to scalar
  with GPU min reduction, adap_dt_stop_sum atomic approach, bubbles_lagrange
  MPI reduction inside master's block structure
- Accept master's additions: ib_state_unit, nt_step in post_process

Author: sbryngelson

.github/workflows/claude-code-review.yml

@@ -2,7 +2,7 @@ name: Claude Code Review
 
 on:
   pull_request_target:
-    types: [opened, synchronize, ready_for_review, reopened, labeled]
+    types: [opened, ready_for_review, reopened, labeled]
   issue_comment:
     types: [created]
 
@@ -15,7 +15,6 @@ jobs:
           github.event.action == 'opened' ||
           github.event.action == 'ready_for_review' ||
           github.event.action == 'reopened' ||
-          github.event.action == 'synchronize' ||
           (
             github.event.action == 'labeled' &&
             github.event.label.name == 'claude-full-review'
@@ -42,47 +41,40 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y unzip jq
 
-      - name: Checkout base repo
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-
-      - name: Determine PR number and requested review mode
+      - name: Determine PR number
         id: mode
         shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
         run: |
           set -euo pipefail
 
           if [[ "${{ github.event_name }}" == "pull_request_target" ]]; then
             PR_NUMBER="${{ github.event.pull_request.number }}"
-            case "${{ github.event.action }}" in
-              opened|ready_for_review|reopened)
-                REQUESTED_MODE="full"
-                ;;
-              synchronize)
-                REQUESTED_MODE="incremental"
-                ;;
-              labeled)
-                if [[ "${{ github.event.label.name }}" == "claude-full-review" ]]; then
-                  REQUESTED_MODE="full"
-                else
-                  REQUESTED_MODE="full"
-                fi
-                ;;
-              *)
-                REQUESTED_MODE="full"
-                ;;
-            esac
           elif [[ "${{ github.event_name }}" == "issue_comment" ]]; then
             PR_NUMBER="${{ github.event.issue.number }}"
-            REQUESTED_MODE="full"
           else
             echo "Unsupported event"
             exit 1
           fi
 
+          PR_HEAD_REF="$(gh pr view "$PR_NUMBER" --repo "${{ github.repository }}" --json headRefName --jq .headRefName)"
+
           echo "pr_number=$PR_NUMBER" >> "$GITHUB_OUTPUT"
-          echo "requested_mode=$REQUESTED_MODE" >> "$GITHUB_OUTPUT"
+          echo "pr_head_ref=$PR_HEAD_REF" >> "$GITHUB_OUTPUT"
+
+      - name: Checkout base repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Fetch PR branch
+        shell: bash
+        env:
+          PR_HEAD_REF: ${{ steps.mode.outputs.pr_head_ref }}
+        run: |
+          set -euo pipefail
+          git fetch origin "$PR_HEAD_REF"
 
       - name: Resolve review state
         id: state
@@ -94,7 +86,6 @@ jobs:
 
           PR_NUMBER="${{ steps.mode.outputs.pr_number }}"
           REPO="${{ github.repository }}"
-          REQUESTED_MODE="${{ steps.mode.outputs.requested_mode }}"
 
           mkdir -p .claude-review/context
 
@@ -108,23 +99,13 @@ jobs:
           )"
 
           EXISTING_COMMENT_ID=""
-          PREVIOUS_REVIEWED_SHA=""
 
           if [[ -n "${LAST_COMMENT_B64:-}" ]]; then
             LAST_COMMENT_JSON="$(printf '%s' "$LAST_COMMENT_B64" | base64 -d)"
             EXISTING_COMMENT_ID="$(printf '%s' "$LAST_COMMENT_JSON" | jq -r '.id // empty')"
-            COMMENT_BODY="$(printf '%s' "$LAST_COMMENT_JSON" | jq -r '.body // empty')"
-            PREVIOUS_REVIEWED_SHA="$(printf '%s' "$COMMENT_BODY" | sed -n 's/.*reviewed_sha=\([0-9a-fA-F]\{7,\}\).*/\1/p' | tail -n1)"
-          fi
-
-          EFFECTIVE_MODE="$REQUESTED_MODE"
-          if [[ "$REQUESTED_MODE" == "incremental" && -z "${PREVIOUS_REVIEWED_SHA:-}" ]]; then
-            EFFECTIVE_MODE="full"
           fi
 
           echo "existing_comment_id=${EXISTING_COMMENT_ID:-}" >> "$GITHUB_OUTPUT"
-          echo "previous_reviewed_sha=${PREVIOUS_REVIEWED_SHA:-}" >> "$GITHUB_OUTPUT"
-          echo "effective_mode=$EFFECTIVE_MODE" >> "$GITHUB_OUTPUT"
 
       - name: Build review diff and changed-file list
         id: review_input
@@ -136,43 +117,23 @@ jobs:
 
           PR_NUMBER="${{ steps.mode.outputs.pr_number }}"
           REPO="${{ github.repository }}"
-          MODE="${{ steps.state.outputs.effective_mode }}"
-          CURRENT_SHA="${{ steps.state.outputs.current_head_sha }}"
-          PREV_SHA="${{ steps.state.outputs.previous_reviewed_sha }}"
 
           mkdir -p .claude-review
-          : > .claude-review/review.diff
-          : > .claude-review/changed_files.txt
 
-          build_full() {
-            gh pr diff "$PR_NUMBER" --repo "$REPO" > .claude-review/review.diff
-            gh pr view "$PR_NUMBER" --repo "$REPO" --json files --jq '.files[].path' > .claude-review/changed_files.txt
-            echo "actual_mode=full" >> "$GITHUB_OUTPUT"
-          }
+          gh pr diff "$PR_NUMBER" --repo "$REPO" > .claude-review/review.diff.raw
+          gh pr view "$PR_NUMBER" --repo "$REPO" --json files --jq '.files[].path' > .claude-review/changed_files.txt.raw
 
-          if [[ "$MODE" == "full" ]]; then
-            build_full
-          else
-            if gh api -H "Accept: application/vnd.github.diff" \
-              "repos/$REPO/compare/$PREV_SHA...$CURRENT_SHA" > .claude-review/review.diff.tmp 2>/dev/null \
-              && gh api "repos/$REPO/compare/$PREV_SHA...$CURRENT_SHA" --jq '.files[].filename' > .claude-review/changed_files.txt.tmp 2>/dev/null; then
-              mv .claude-review/review.diff.tmp .claude-review/review.diff
-              mv .claude-review/changed_files.txt.tmp .claude-review/changed_files.txt
-              echo "actual_mode=incremental" >> "$GITHUB_OUTPUT"
-            else
-              echo "Compare diff failed; falling back to full review."
-              build_full
-            fi
-          fi
+          # Filter out tests/ directory — golden files don't need code review
+          grep -v '^tests/' .claude-review/changed_files.txt.raw > .claude-review/changed_files.txt || true
+          # Strip diff hunks for tests/ files
+          awk '
+            /^diff --git a\/tests\// { skip=1; next }
+            /^diff --git /           { skip=0 }
+            !skip                    { print }
+          ' .claude-review/review.diff.raw > .claude-review/review.diff
 
           sed -i '/^[[:space:]]*$/d' .claude-review/changed_files.txt || true
 
-          if [[ ! -s .claude-review/review.diff ]] || [[ ! -s .claude-review/changed_files.txt ]]; then
-            echo "Prepared diff or changed file list is empty; falling back to full review."
-            build_full
-            sed -i '/^[[:space:]]*$/d' .claude-review/changed_files.txt || true
-          fi
-
           echo "review_diff_path=.claude-review/review.diff" >> "$GITHUB_OUTPUT"
           echo "changed_files_path=.claude-review/changed_files.txt" >> "$GITHUB_OUTPUT"
 
@@ -190,6 +151,10 @@ jobs:
 
           mkdir -p .claude-review/context
 
+          # Prioritize src/ files for context (most likely to need review)
+          sort -t/ -k1,1 -s < "${{ steps.review_input.outputs.changed_files_path }}" | \
+            awk '/^src\//{print; next} {rest[NR]=$0} END{for(i in rest) print rest[i]}' > .claude-review/sorted_files.txt
+
           while IFS= read -r path; do
             [[ -z "$path" ]] && continue
             COUNT=$((COUNT + 1))
@@ -206,10 +171,10 @@ jobs:
             [[ -z "$CONTENT" ]] && continue
 
             LINE_COUNT="$(printf '%s' "$CONTENT" | wc -l | tr -d ' ')"
-            if [[ "$LINE_COUNT" -le 400 ]]; then
+            if [[ "$LINE_COUNT" -le 1500 ]]; then
               printf '%s' "$CONTENT" > ".claude-review/context/$SAFE_NAME"
             fi
-          done < "${{ steps.review_input.outputs.changed_files_path }}"
+          done < .claude-review/sorted_files.txt
 
           echo "context_dir=.claude-review/context" >> "$GITHUB_OUTPUT"
 
@@ -221,6 +186,7 @@ jobs:
           : > .claude-review/output.md
 
       - name: Run Claude Code Review
+        continue-on-error: true
         uses: anthropics/claude-code-action@v1
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
@@ -229,16 +195,13 @@ jobs:
           plugins: "code-review@claude-code-plugins"
           claude_args: >
             --dangerously-skip-permissions
-            --max-turns 90
+            --max-turns 40
             --allowedTools
             "Bash"
           prompt: |
             You are running in GitHub Actions review automation.
 
-            REQUESTED REVIEW MODE: ${{ steps.state.outputs.effective_mode }}
-            ACTUAL REVIEW MODE: ${{ steps.review_input.outputs.actual_mode }}
             PR NUMBER: ${{ steps.mode.outputs.pr_number }}
-            PREVIOUS REVIEWED SHA: ${{ steps.state.outputs.previous_reviewed_sha }}
             CURRENT HEAD SHA: ${{ steps.state.outputs.current_head_sha }}
 
             Review ONLY the prepared inputs for this run.
@@ -264,7 +227,7 @@ jobs:
             - Nearby unchanged lines in changed files may be used as supporting context only.
             - Do NOT raise findings about code outside changed files.
             - Do NOT provide general repo suggestions or unrelated improvement ideas.
-            - Do NOT include positive confirmations like "No issues with X".
+            - Do NOT include positive confirmations like "No issues with X"
             - If confidence is low, omit the finding.
 
             Allowed workflow:
@@ -278,23 +241,25 @@ jobs:
             8) Do NOT post, update, or create GitHub comments yourself
 
             Review policy:
-            - In full mode, review the full PR diff.
-            - In incremental mode, review only the delta diff.
-            - In incremental mode, report only new issues introduced by that delta.
-            - Do NOT repeat earlier findings.
+            - Review the full PR diff.
             - Do NOT restate the full PR summary.
             - If there are no high-confidence findings, leave .claude-review/output.md empty and STOP.
 
-            Review standard:
-            - Prefer correctness, reliability, cleanup/finalization gaps, inconsistent behavior, edge cases, and meaningful test gaps.
+            Review standard (in priority order per CLAUDE.md "Code Review Priorities"):
+            1. Correctness (logic bugs, numerical issues, array bounds)
+            2. Precision discipline (stp vs wp mixing)
+            3. Memory management (@:ALLOCATE/@:DEALLOCATE pairing, GPU pointer setup)
+            4. MPI correctness (halo exchange, buffer sizing, GPU_UPDATE calls)
+            5. GPU code (GPU_* Fypp macros only, no raw pragmas)
+            6. Physics consistency (pressure formula matches model_eqns)
+            7. Compiler portability (4 CI-gated compilers + AMD flang for GPU)
             - Avoid style nitpicks.
             - A finding is valid only if it is supported by changed lines, with changed-file context used only to confirm it.
 
             Output rules:
             - Write markdown only to .claude-review/output.md
-            - If there are findings, use exactly one of these formats.
+            - If there are findings, use exactly this format:
 
-            For full mode:
             Claude Code Review
 
             Head SHA: <sha>
@@ -308,17 +273,6 @@ jobs:
 
             <!-- claude-review: thread=primary; reviewed_sha=<current_head_sha>; mode=full -->
 
-            For incremental mode:
-            Claude Code Review
-
-            Incremental review from: <previous_sha>
-            Head SHA: <current_sha>
-
-            New findings since last Claude review:
-            - <only high-confidence issues grounded in changed hunks of the delta diff>
-
-            <!-- claude-review: thread=primary; reviewed_sha=<current_head_sha>; mode=incremental -->
-
             - Always include the hidden marker exactly once at the end of the file.
             - If there are no findings, write nothing.