msd-core/commands/gsd/reapply-patches.md

---
name: gsd:reapply-patches
description: Reapply local modifications after a GSD update
allowed-tools: Read, Write, Edit, Bash, Glob, Grep, AskUserQuestion
---

<purpose>
After a GSD update wipes and reinstalls files, this command merges user's previously saved local modifications back into the new version. Uses three-way comparison (pristine baseline, user-modified backup, newly installed version) to reliably distinguish user customizations from version drift.

**Critical invariant:** Every file in `gsd-local-patches/` was backed up because the installer's hash comparison detected it was modified. The workflow must NEVER conclude "no custom content" for any backed-up file — that is a logical contradiction. When in doubt, classify as CONFLICT requiring user review, not SKIP.
</purpose>

<process>

## Step 1: Detect backed-up patches

Check for local patches directory:

```bash
expand_home() {
  case "$1" in
    "~/"*) printf '%s/%s\n' "$HOME" "${1#~/}" ;;
    *) printf '%s\n' "$1" ;;
  esac
}

PATCHES_DIR=""

# Env overrides first — covers custom config directories used with --config-dir
if [ -n "$KILO_CONFIG_DIR" ]; then
  candidate="$(expand_home "$KILO_CONFIG_DIR")/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
elif [ -n "$KILO_CONFIG" ]; then
  candidate="$(dirname "$(expand_home "$KILO_CONFIG")")/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
elif [ -n "$XDG_CONFIG_HOME" ]; then
  candidate="$(expand_home "$XDG_CONFIG_HOME")/kilo/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
fi

if [ -z "$PATCHES_DIR" ] && [ -n "$OPENCODE_CONFIG_DIR" ]; then
  candidate="$(expand_home "$OPENCODE_CONFIG_DIR")/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
elif [ -z "$PATCHES_DIR" ] && [ -n "$OPENCODE_CONFIG" ]; then
  candidate="$(dirname "$(expand_home "$OPENCODE_CONFIG")")/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
elif [ -z "$PATCHES_DIR" ] && [ -n "$XDG_CONFIG_HOME" ]; then
  candidate="$(expand_home "$XDG_CONFIG_HOME")/opencode/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
fi

if [ -z "$PATCHES_DIR" ] && [ -n "$GEMINI_CONFIG_DIR" ]; then
  candidate="$(expand_home "$GEMINI_CONFIG_DIR")/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
fi

if [ -z "$PATCHES_DIR" ] && [ -n "$CODEX_HOME" ]; then
  candidate="$(expand_home "$CODEX_HOME")/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
fi

if [ -z "$PATCHES_DIR" ] && [ -n "$CLAUDE_CONFIG_DIR" ]; then
  candidate="$(expand_home "$CLAUDE_CONFIG_DIR")/gsd-local-patches"
  if [ -d "$candidate" ]; then
    PATCHES_DIR="$candidate"
  fi
fi

# Global install — detect runtime config directory defaults
if [ -z "$PATCHES_DIR" ]; then
  if [ -d "$HOME/.config/kilo/gsd-local-patches" ]; then
    PATCHES_DIR="$HOME/.config/kilo/gsd-local-patches"
  elif [ -d "$HOME/.config/opencode/gsd-local-patches" ]; then
    PATCHES_DIR="$HOME/.config/opencode/gsd-local-patches"
  elif [ -d "$HOME/.opencode/gsd-local-patches" ]; then
    PATCHES_DIR="$HOME/.opencode/gsd-local-patches"
  elif [ -d "$HOME/.gemini/gsd-local-patches" ]; then
    PATCHES_DIR="$HOME/.gemini/gsd-local-patches"
  elif [ -d "$HOME/.codex/gsd-local-patches" ]; then
    PATCHES_DIR="$HOME/.codex/gsd-local-patches"
  else
    PATCHES_DIR="$HOME/.claude/gsd-local-patches"
  fi
fi
# Local install fallback — check all runtime directories
if [ ! -d "$PATCHES_DIR" ]; then
  for dir in .config/kilo .kilo .config/opencode .opencode .gemini .codex .claude; do
    if [ -d "./$dir/gsd-local-patches" ]; then
      PATCHES_DIR="./$dir/gsd-local-patches"
      break
    fi
  done
fi
```

Read `backup-meta.json` from the patches directory.

**If no patches found:**
```
No local patches found. Nothing to reapply.

Local patches are automatically saved when you run /gsd-update
after modifying any GSD workflow, command, or agent files.
```
Exit.

## Step 2: Determine baseline for three-way comparison

The quality of the merge depends on having a **pristine baseline** — the original unmodified version of each file from the pre-update GSD release. This enables three-way comparison:
- **Pristine baseline** (original GSD file before any user edits)
- **User's version** (backed up in `gsd-local-patches/`)
- **New version** (freshly installed after update)

Check for baseline sources in priority order:

### Option A: Pristine hash from backup-meta.json + git history (most reliable)
If the config directory is a git repository:
```bash
CONFIG_DIR=$(dirname "$PATCHES_DIR")
if git -C "$CONFIG_DIR" rev-parse --git-dir >/dev/null 2>&1; then
  HAS_GIT=true
fi
```
When `HAS_GIT=true`, use the `pristine_hashes` recorded in `backup-meta.json` to locate the correct baseline commit. For each file, iterate commits that touched it and find the one whose blob SHA-256 matches the recorded pristine hash:
```bash
# Get the expected pristine SHA-256 from backup-meta.json
PRISTINE_HASH=$(jq -r ".pristine_hashes[\"${file_path}\"] // empty" "$PATCHES_DIR/backup-meta.json")

BASELINE_COMMIT=""
if [ -n "$PRISTINE_HASH" ]; then
  # Walk commits that touched this file, pick the one matching the pristine hash
  while IFS= read -r commit_hash; do
    blob_hash=$(git -C "$CONFIG_DIR" show "${commit_hash}:${file_path}" 2>/dev/null | sha256sum | cut -d' ' -f1)
    if [ "$blob_hash" = "$PRISTINE_HASH" ]; then
      BASELINE_COMMIT="$commit_hash"
      break
    fi
  done < <(git -C "$CONFIG_DIR" log --format="%H" -- "${file_path}")
fi

# Fallback: if no pristine hash in backup-meta (older installer), use first-add commit
if [ -z "$BASELINE_COMMIT" ]; then
  BASELINE_COMMIT=$(git -C "$CONFIG_DIR" log --diff-filter=A --format="%H" -- "${file_path}" | tail -1)
fi
```
Extract the pristine version from the matched commit:
```bash
git -C "$CONFIG_DIR" show "${BASELINE_COMMIT}:${file_path}"
```

**Why this matters:** `git log --diff-filter=A` returns the commit that *first added* the file, which is the wrong baseline on repos that have been through multiple GSD update cycles. The `pristine_hashes` field in `backup-meta.json` records the SHA-256 of the file as it existed in the pre-update GSD release — matching against it finds the correct baseline regardless of how many updates have occurred.

### Option B: Pristine snapshot directory
Check if a `gsd-pristine/` directory exists alongside `gsd-local-patches/`:
```bash
PRISTINE_DIR="$CONFIG_DIR/gsd-pristine"
```
If it exists, the installer saved pristine copies at install time. Use these as the baseline.

### Option C: No baseline available (two-way fallback)
If neither git history nor pristine snapshots are available, fall back to two-way comparison — but with **strengthened heuristics** (see Step 3).

## Step 3: Show patch summary

```
## Local Patches to Reapply

**Backed up from:** v{from_version}
**Current version:** {read VERSION file}
**Files modified:** {count}
**Merge strategy:** {three-way (git) | three-way (pristine) | two-way (enhanced)}

| # | File | Status |
|---|------|--------|
| 1 | {file_path} | Pending |
| 2 | {file_path} | Pending |
```

## Step 4: Merge each file

For each file in `backup-meta.json`:

1. **Read the backed-up version** (user's modified copy from `gsd-local-patches/`)
2. **Read the newly installed version** (current file after update)
3. **If available, read the pristine baseline** (from git history or `gsd-pristine/`)

### Three-way merge (when baseline is available)

Compare the three versions to isolate changes:
- **User changes** = diff(pristine → user's version) — these are the customizations to preserve
- **Upstream changes** = diff(pristine → new version) — these are version updates to accept

**Merge rules:**
- Sections changed only by user → apply user's version
- Sections changed only by upstream → accept upstream version
- Sections changed by both → flag as CONFLICT, show both, ask user
- Sections unchanged by either → use new version (identical to all three)

### Two-way merge (fallback when no baseline)

When no pristine baseline is available, use these **strengthened heuristics**:

**CRITICAL RULE: Every file in this backup directory was explicitly detected as modified by the installer's SHA-256 hash comparison. "No custom content" is never a valid conclusion.**

For each file:
a. Read both versions completely
b. Identify ALL differences, then classify each as:
   - **Mechanical drift** — path substitutions (e.g. `/Users/xxx/.claude/` → `$HOME/.claude/`), variable additions (`${GSD_WS}`, `${AGENT_SKILLS_*}`), error handling additions (`|| true`)
   - **User customization** — added steps/sections, removed sections, reordered content, changed behavior, added frontmatter fields, modified instructions

c. **If ANY differences remain after filtering out mechanical drift → those are user customizations. Merge them.**
d. **If ALL differences appear to be mechanical drift → still flag as CONFLICT.** The installer's hash check already proved this file was modified. Ask the user: "This file appears to only have path/variable differences. Were there intentional customizations?" Do NOT silently skip.

### Git-enhanced two-way merge

When the config directory is a git repo but the pristine install commit can't be found, use commit history to identify user changes:
```bash
# Find non-update commits that touched this file
git -C "$CONFIG_DIR" log --oneline --no-merges -- "{file_path}" | grep -v "gsd:update\|GSD update\|gsd-install"
```
Each matching commit represents an intentional user modification. Use the commit messages and diffs to understand what was changed and why.

4. **Write merged result** to the installed location

### Post-merge verification

After writing each merged file, verify that user modifications survived the merge:

1. **Line-count check:** Count lines in the backup and the merged result. If the merged result has fewer lines than the backup minus the expected upstream removals, flag for review.
2. **Hunk presence check:** For each user-added section identified during diff analysis, search the merged output for at least the first significant line (non-blank, non-comment) of each addition. Missing signature lines indicate a dropped hunk.
3. **Report warnings inline** (do not block):
   ```
   ⚠ Potential dropped content in {file_path}:
     - Missing hunk near line {N}: "{first_line_preview}..." ({line_count} lines)
     - Backup available: {patches_dir}/{file_path}
   ```
4. **Produce a Hunk Verification Table** — one row per hunk per file. This table is **mandatory output** and must be produced before Step 5 can proceed. Format:

   | file | hunk_id | signature_line | line_count | verified |
   |------|---------|----------------|------------|----------|
   | {file_path} | {N} | {first_significant_line} | {count} | yes |
   | {file_path} | {N} | {first_significant_line} | {count} | no |

   - `hunk_id` — sequential integer per file (1, 2, 3…)
   - `signature_line` — first non-blank, non-comment line of the user-added section
   - `line_count` — total lines in the hunk
   - `verified` — `yes` if the signature_line is present in the merged output, `no` otherwise

5. **Track verification status** — add to per-file report: `Merged (verified)` vs `Merged (⚠ {N} hunks may be missing)`

6. **Report status per file:**
   - `Merged` — user modifications applied cleanly (show summary of what was preserved)
   - `Conflict` — user reviewed and chose resolution
   - `Incorporated` — user's modification was already adopted upstream (only valid when pristine baseline confirms this)

**Never report `Skipped — no custom content`.** If a file is in the backup, it has custom content.

## Step 5: Hunk Verification Gate

Before proceeding to cleanup, evaluate the Hunk Verification Table produced in Step 4.

**If the Hunk Verification Table is absent** (Step 4 did not produce it), STOP immediately and report to the user:
```
ERROR: Hunk Verification Table is missing. Post-merge verification was not completed.
Rerun /gsd-reapply-patches to retry with full verification.
```

**If any row in the Hunk Verification Table shows `verified: no`**, STOP and report to the user:
```
ERROR: {N} hunk(s) failed verification — content may have been dropped during merge.

Unverified hunks:
  {file} hunk {hunk_id}: signature line "{signature_line}" not found in merged output

The backup is preserved at: {patches_dir}/{file}
Review the merged file manually, then either:
  (a) Re-merge the missing content by hand, or
  (b) Restore from backup: cp {patches_dir}/{file} {installed_path}
```

Do not proceed to cleanup until the user confirms they have resolved all unverified hunks.

**Only when all rows show `verified: yes`** (or when all files had zero user-added hunks) may execution continue to Step 6.

## Step 6: Cleanup option

Ask user:
- "Keep patch backups for reference?" → preserve `gsd-local-patches/`
- "Clean up patch backups?" → remove `gsd-local-patches/` directory

## Step 7: Report

```
## Patches Reapplied

| # | File | Result | User Changes Preserved |
|---|------|--------|----------------------|
| 1 | {file_path} | Merged | Added step X, modified section Y |
| 2 | {file_path} | Incorporated | Already in upstream v{version} |
| 3 | {file_path} | Conflict resolved | User chose: keep custom section |

{count} file(s) updated. Your local modifications are active again.
```

</process>

<success_criteria>
- [ ] All backed-up patches processed — zero files left unhandled
- [ ] No file classified as "no custom content" or "SKIP" — every backed-up file is definitionally modified
- [ ] Three-way merge used when pristine baseline available (git history or gsd-pristine/)
- [ ] User modifications identified and merged into new version
- [ ] Conflicts surfaced to user with both versions shown
- [ ] Status reported for each file with summary of what was preserved
- [ ] Post-merge verification checks each file for dropped hunks and warns if content appears missing
</success_criteria>