Merge pull request #1474 from Tibsfox/fix/reapply-patches-misclassification-1469
fix(reapply-patches): three-way merge and never-skip invariant for backed-up files
This commit is contained in:
Tom Boucher
@@ -4,7 +4,9 @@ allowed-tools: Read, Write, Edit, Bash, Glob, Grep, AskUserQuestion
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---
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<purpose>
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After a GSD update wipes and reinstalls files, this command merges user's previously saved local modifications back into the new version. Uses intelligent comparison to handle cases where the upstream file also changed.
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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.
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**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.
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</purpose>
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<process>
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@@ -46,7 +48,43 @@ after modifying any GSD workflow, command, or agent files.
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```
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Exit.
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## Step 2: Show patch summary
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## Step 2: Determine baseline for three-way comparison
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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:
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- **Pristine baseline** (original GSD file before any user edits)
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- **User's version** (backed up in `gsd-local-patches/`)
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- **New version** (freshly installed after update)
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Check for baseline sources in priority order:
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### Option A: Git history (most reliable)
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If the config directory is a git repository:
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```bash
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CONFIG_DIR=$(dirname "$PATCHES_DIR")
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if git -C "$CONFIG_DIR" rev-parse --git-dir >/dev/null 2>&1; then
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HAS_GIT=true
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fi
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```
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When `HAS_GIT=true`, use `git log` to find the commit where GSD was originally installed (before user edits). For each file, the pristine baseline can be extracted with:
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```bash
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git -C "$CONFIG_DIR" log --diff-filter=A --format="%H" -- "{file_path}"
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```
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This gives the commit that first added the file (the install commit). Extract the pristine version:
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```bash
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git -C "$CONFIG_DIR" show {install_commit}:{file_path}
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```
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### Option B: Pristine snapshot directory
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Check if a `gsd-pristine/` directory exists alongside `gsd-local-patches/`:
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```bash
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PRISTINE_DIR="$CONFIG_DIR/gsd-pristine"
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```
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If it exists, the installer saved pristine copies at install time. Use these as the baseline.
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### Option C: No baseline available (two-way fallback)
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If neither git history nor pristine snapshots are available, fall back to two-way comparison — but with **strengthened heuristics** (see Step 3).
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## Step 3: Show patch summary
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```
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## Local Patches to Reapply
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@@ -54,6 +92,7 @@ Exit.
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**Backed up from:** v{from_version}
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**Current version:** {read VERSION file}
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**Files modified:** {count}
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**Merge strategy:** {three-way (git) | three-way (pristine) | two-way (enhanced)}
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| # | File | Status |
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|---|------|--------|
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@@ -61,30 +100,59 @@ Exit.
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| 2 | {file_path} | Pending |
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```
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## Step 3: Merge each file
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## Step 4: Merge each file
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For each file in `backup-meta.json`:
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1. **Read the backed-up version** (user's modified copy from `gsd-local-patches/`)
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2. **Read the newly installed version** (current file after update)
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3. **Compare and merge:**
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3. **If available, read the pristine baseline** (from git history or `gsd-pristine/`)
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- If the new file is identical to the backed-up file: skip (modification was incorporated upstream)
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- If the new file differs: identify the user's modifications and apply them to the new version
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### Three-way merge (when baseline is available)
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**Merge strategy:**
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- Read both versions fully
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- Identify sections the user added or modified (look for additions, not just differences from path replacement)
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- Apply user's additions/modifications to the new version
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- If a section the user modified was also changed upstream: flag as conflict, show both versions, ask user which to keep
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Compare the three versions to isolate changes:
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- **User changes** = diff(pristine → user's version) — these are the customizations to preserve
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- **Upstream changes** = diff(pristine → new version) — these are version updates to accept
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**Merge rules:**
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- Sections changed only by user → apply user's version
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- Sections changed only by upstream → accept upstream version
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- Sections changed by both → flag as CONFLICT, show both, ask user
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- Sections unchanged by either → use new version (identical to all three)
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### Two-way merge (fallback when no baseline)
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When no pristine baseline is available, use these **strengthened heuristics**:
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**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.**
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For each file:
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a. Read both versions completely
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b. Identify ALL differences, then classify each as:
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- **Mechanical drift** — path substitutions (e.g. `/Users/xxx/.claude/` → `$HOME/.claude/`), variable additions (`${GSD_WS}`, `${AGENT_SKILLS_*}`), error handling additions (`|| true`)
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- **User customization** — added steps/sections, removed sections, reordered content, changed behavior, added frontmatter fields, modified instructions
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c. **If ANY differences remain after filtering out mechanical drift → those are user customizations. Merge them.**
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d. **If ALL differences appear to be mechanical drift → still flag as CONFLICT.** The installer's hash check already proved this file was modified. Ask the user: "This file appears to only have path/variable differences. Were there intentional customizations?" Do NOT silently skip.
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### Git-enhanced two-way merge
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When the config directory is a git repo but the pristine install commit can't be found, use commit history to identify user changes:
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```bash
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# Find non-update commits that touched this file
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git -C "$CONFIG_DIR" log --oneline --no-merges -- "{file_path}" | grep -v "gsd:update\|GSD update\|gsd-install"
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```
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Each matching commit represents an intentional user modification. Use the commit messages and diffs to understand what was changed and why.
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4. **Write merged result** to the installed location
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5. **Report status:**
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- `Merged` — user modifications applied cleanly
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- `Skipped` — modification already in upstream
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- `Conflict` — user chose resolution
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5. **Report status per file:**
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- `Merged` — user modifications applied cleanly (show summary of what was preserved)
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- `Conflict` — user reviewed and chose resolution
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- `Incorporated` — user's modification was already adopted upstream (only valid when pristine baseline confirms this)
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## Step 4: Update manifest
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**Never report `Skipped — no custom content`.** If a file is in the backup, it has custom content.
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## Step 5: Update manifest
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After reapplying, regenerate the file manifest so future updates correctly detect these as user modifications:
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@@ -93,22 +161,22 @@ After reapplying, regenerate the file manifest so future updates correctly detec
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# For now, just note which files were modified
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```
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## Step 5: Cleanup option
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## Step 6: Cleanup option
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Ask user:
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- "Keep patch backups for reference?" → preserve `gsd-local-patches/`
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- "Clean up patch backups?" → remove `gsd-local-patches/` directory
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## Step 6: Report
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## Step 7: Report
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```
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## Patches Reapplied
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| # | File | Status |
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|---|------|--------|
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| 1 | {file_path} | ✓ Merged |
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| 2 | {file_path} | ○ Skipped (already upstream) |
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| 3 | {file_path} | ⚠ Conflict resolved |
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| # | File | Result | User Changes Preserved |
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|---|------|--------|----------------------|
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| 1 | {file_path} | Merged | Added step X, modified section Y |
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| 2 | {file_path} | Incorporated | Already in upstream v{version} |
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| 3 | {file_path} | Conflict resolved | User chose: keep custom section |
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{count} file(s) updated. Your local modifications are active again.
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```
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@@ -116,8 +184,10 @@ Ask user:
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</process>
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<success_criteria>
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- [ ] All backed-up patches processed
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- [ ] User modifications merged into new version
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- [ ] Conflicts resolved with user input
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- [ ] Status reported for each file
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- [ ] All backed-up patches processed — zero files left unhandled
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- [ ] No file classified as "no custom content" or "SKIP" — every backed-up file is definitionally modified
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- [ ] Three-way merge used when pristine baseline available (git history or gsd-pristine/)
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- [ ] User modifications identified and merged into new version
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- [ ] Conflicts surfaced to user with both versions shown
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- [ ] Status reported for each file with summary of what was preserved
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</success_criteria>
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