Handle merge conflicts in merge-fix workflow

.agents/skills/merge/resolve-conflicts.md

@@ -1,61 +1,70 @@
-# Resolve Merge Conflicts
+# Verify Merge Conflict Resolutions
 
-Resolve merge conflicts from merging `main` into the `next` branch.
+Verify that the automated conflict resolution (which kept the "ours"/next side for JSON and YAML files) was correct, and fix any issues.
 
 **SCOPE: Do not spawn tasks/sub-agents.**
 
 ## Prerequisites
 
 - **`prNumber`** — The PR number for the merge PR.
 - **`branch`** — The branch name (e.g., `ci/merge-main-to-next`).
-- The working directory is the repo root, checked out on the merge branch with conflict markers present.
+- The working directory is the repo root, checked out on the merge branch.
+- Dependencies are installed and packages are built.
+- Conflict markers in JSON/YAML files have already been stripped by the GitHub Action, keeping the "ours" (next) side. Source code files (`.ts`, `.js`, `.md`, `.astro`) may still have conflict markers.
 
-## Strategy
+## Background
 
-When resolving conflicts, follow these rules based on file type:
+The GitHub Action strips conflict markers from JSON/YAML files before `pnpm install` can run, always keeping the `next` branch side. This is usually correct (next has pre-release versions that must be preserved), but it may discard important changes from `main` — like new dependencies, updated dependency versions, or config changes from bug fixes.
 
-### Changeset files (`.changeset/*.md`)
+## Steps
 
-- If a changeset file exists on `main` but not on `next`, it was likely already released. **Delete it.** The clean-changesets skill will handle this more thoroughly, but removing obvious ones here unblocks the merge.
-- If both branches modified the same changeset, prefer the `next` version since it's the one targeting the upcoming major.
+### Step 1: Resolve any remaining conflict markers
 
-### `package.json` and version files
+Check for conflict markers in source code files:
 
-- **Prefer `next` branch versions.** The `next` branch has the pre-release versions (alpha/beta) which should not be overwritten by `main`'s stable versions.
-- For dependency version updates from `main`, accept those — they are typically patches/minors that should be forward-ported.
+```bash
+grep -r "<<<<<<< " --include="*.ts" --include="*.js" --include="*.mjs" --include="*.cjs" --include="*.md" --include="*.astro" . 2>/dev/null | grep -v node_modules
+```
 
-### `pnpm-lock.yaml`
+If any exist, resolve them following these rules:
+- **Prefer `main` for bug fixes.** If `main` fixed a bug, that fix should carry over to `next`.
+- **Prefer `next` for API changes.** If `next` changed an API, keep the `next` version and adapt the `main` fix if needed.
+- When in doubt, prefer `next` — it's the forward-looking branch.
 
-- Do not try to manually resolve lockfile conflicts. Instead:
-  1. Accept the `next` version: `git checkout --theirs pnpm-lock.yaml`
-  2. The lockfile will be regenerated after `pnpm install` later.
+After resolving, `git add` each file.
 
-### Source code (`packages/**/*.ts`, `packages/**/*.js`)
+### Step 2: Review what was lost from main
 
-- **Prefer `main` for bug fixes.** If `main` fixed a bug, that fix should carry over to `next`.
-- **Prefer `next` for API changes.** If `next` changed an API (new major version features), keep the `next` version and adapt the `main` fix to work with it if needed.
-- When in doubt, prefer `next` — it's the forward-looking branch.
+Compare what `main` had in the conflicted files against what we kept:
 
-### Test files
+```bash
+# List files that were modified on both branches (potential conflict sites)
+git diff --name-only origin/next...origin/main -- '*.json' '*.yaml' '*.yml'
+```
 
-- If tests conflict, prefer `next` and adapt. Tests on `next` may test new major-version behavior.
+For each file, compare the `main` version to the current version:
 
-### Configuration files (`.changeset/config.json`, `tsconfig.json`, etc.)
+```bash
+git diff origin/main -- <file>
+```
 
-- Prefer `next` unless `main` has a clear fix that should be forward-ported.
+Look for:
+- **New dependencies** added on `main` that are missing from `next` — these should be added
+- **Dependency version bumps** on `main` that are higher than what's on `next` — these should typically be accepted (they're patches/minors)
+- **New scripts or config entries** added on `main` — these should be forward-ported
+- **Version fields** (`"version":`) — keep `next`'s pre-release versions, do NOT use `main`'s stable versions
 
-## Steps
+### Step 3: Apply corrections
+
+If you find changes from `main` that should have been kept:
+1. Apply those specific changes to the current files
+2. Run `pnpm install --no-frozen-lockfile` if you modified any `package.json` files
+3. `git add` the modified files
+
+### Step 4: Do NOT commit
 
-1. Run `git diff --name-only --diff-filter=U` to list all conflicted files.
-2. For each conflicted file, read the file and resolve the conflict following the strategy above.
-3. After resolving each file, run `git add <file>` to mark it as resolved.
-4. After all files are resolved, verify no conflict markers remain: `grep -r "<<<<<<< " --include="*.ts" --include="*.js" --include="*.json" --include="*.yaml" --include="*.yml" --include="*.md" .`
-5. After conflicts are resolved, regenerate the lockfile and install dependencies:
-   ```bash
-   pnpm install --no-frozen-lockfile
-   ```
-6. Do NOT commit — the orchestrator will handle committing.
+The orchestrator will handle committing.
 
 ## Output
 
-Return the list of files that were resolved and whether all conflicts were successfully handled.
+Return whether the conflict resolutions were correct and what files (if any) needed corrections.

.flue/workflows/merge-fix/WORKFLOW.ts

@@ -26,37 +26,25 @@ export const args = v.object({
 export default async function mergeFix(flue: FlueClient, { prNumber }: v.InferOutput<typeof args>) {
 	const branch = 'ci/merge-main-to-next';
 
-	// Step 1: Check for merge conflicts (unresolved conflict markers in files)
-	const conflictCheck = await flue.shell(
-		'git diff --check HEAD 2>&1 || grep -r "<<<<<<< " --include="*.ts" --include="*.js" --include="*.json" --include="*.yaml" --include="*.yml" --include="*.md" --include="*.mjs" --include="*.cjs" . 2>/dev/null | head -20',
-	);
-	const hasConflicts = conflictCheck.stdout.includes('<<<<<<<');
-
-	// Step 2: Resolve conflicts if any
-	if (hasConflicts) {
-		await flue.skill('merge/resolve-conflicts.md', {
-			args: { prNumber, branch },
-			result: v.object({
-				resolved: v.pipe(
-					v.boolean(),
-					v.description('true if all merge conflicts were resolved successfully'),
-				),
-				filesResolved: v.pipe(
-					v.array(v.string()),
-					v.description('List of files where conflicts were resolved'),
-				),
-			}),
-		});
-	}
-
-	// Step 3: Ensure dependencies are installed
-	// If conflicts were resolved, the resolve-conflicts skill already ran pnpm install.
-	// If not, we still need to install deps before proceeding.
-	if (!hasConflicts) {
-		await flue.shell('pnpm install --no-frozen-lockfile');
-	}
+	// Step 1: Verify conflict resolutions and resolve any remaining source code conflicts.
+	// JSON/YAML conflicts were pre-stripped by the GitHub Action (keeping next side).
+	// This skill checks that nothing important from main was lost, and resolves
+	// any remaining conflict markers in .ts/.js/.md/.astro files.
+	const verifyResult = await flue.skill('merge/resolve-conflicts.md', {
+		args: { prNumber, branch },
+		result: v.object({
+			correct: v.pipe(
+				v.boolean(),
+				v.description('true if all conflict resolutions were correct or have been fixed'),
+			),
+			correctedFiles: v.pipe(
+				v.array(v.string()),
+				v.description('List of files that needed corrections after verification'),
+			),
+		}),
+	});
 
-	// Step 4: Remove stale changesets that were already released on main
+	// Step 2: Remove stale changesets that were already released on main
 	await flue.skill('merge/clean-changesets.md', {
 		args: { prNumber },
 		result: v.object({
@@ -67,7 +55,7 @@ export default async function mergeFix(flue: FlueClient, { prNumber }: v.InferOu
 		}),
 	});
 
-	// Step 5: Run tests and fix failures
+	// Step 3: Run tests and fix failures
 	const fixResult = await flue.skill('merge/fix-tests.md', {
 		args: { prNumber },
 		result: v.object({
@@ -85,13 +73,13 @@ export default async function mergeFix(flue: FlueClient, { prNumber }: v.InferOu
 		}),
 	});
 
-	// Step 6: Commit and push all changes
+	// Step 4: Commit and push all changes
 	const status = await flue.shell('git status --porcelain');
 	if (status.stdout.trim()) {
 		await flue.shell('git add -A');
 
 		const commitParts = [];
-		if (hasConflicts) commitParts.push('resolve merge conflicts');
+		if (verifyResult.correctedFiles.length > 0) commitParts.push('fix merge conflict resolutions');
 		if (fixResult.fixedFiles.length > 0) commitParts.push('fix test failures');
 		const commitMsg =
 			commitParts.length > 0
@@ -107,9 +95,13 @@ export default async function mergeFix(flue: FlueClient, { prNumber }: v.InferOu
 		}
 	}
 
-	// Step 7: Post a summary comment on the PR
+	// Step 5: Post a summary comment on the PR
 	const summaryParts = [];
-	if (hasConflicts) summaryParts.push('- Resolved merge conflicts');
+	if (verifyResult.correctedFiles.length > 0) {
+		summaryParts.push(
+			`- Fixed conflict resolutions in: ${verifyResult.correctedFiles.join(', ')}`,
+		);
+	}
 	if (fixResult.fixedFiles.length > 0) {
 		summaryParts.push(`- Fixed test failures in: ${fixResult.fixedFiles.join(', ')}`);
 	}
@@ -141,7 +133,7 @@ ${fixResult.testsPass ? 'All tests pass — this PR should be ready for review.'
 	return {
 		pushed: true,
 		testsPass: fixResult.testsPass,
-		hasConflicts,
+		correctedFiles: verifyResult.correctedFiles,
 		remainingFailures: fixResult.remainingFailures,
 	};
 }

.github/workflows/merge-fix.yml

@@ -16,7 +16,6 @@ on:
 
 env:
   IMAGE: ghcr.io/${{ github.repository }}/flue-sandbox
-  PNPM_STORE_DIR: .pnpm-store
 
 concurrency:
   group: merge-fix
@@ -91,6 +90,37 @@ jobs:
             echo "skip=false" >> "$GITHUB_OUTPUT"
           fi
 
+      - name: Strip conflict markers from JSON/YAML files
+        if: steps.pr.outputs.number != '' && steps.attempts.outputs.skip != 'true'
+        # Merge conflicts in package.json files make pnpm install impossible.
+        # Strip conflict markers (keeping "ours"/next side) so pnpm can parse
+        # the workspace. The Flue verify skill will check via git diff whether
+        # anything important from main was lost and patch it back in.
+        run: |
+          node -e '
+            const fs = require("fs");
+            const path = require("path");
+            let count = 0;
+            function fix(dir) {
+              for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+                const full = path.join(dir, entry.name);
+                if (entry.isDirectory() && entry.name !== "node_modules" && entry.name !== ".git") {
+                  fix(full);
+                } else if (/\.(json|yaml|yml)$/.test(entry.name)) {
+                  let c = fs.readFileSync(full, "utf8");
+                  if (c.includes("<<<<<<<")) {
+                    c = c.replace(/^<{7}.*\n([\s\S]*?)^={7}\n[\s\S]*?^>{7}.*\n/gm, "$1");
+                    fs.writeFileSync(full, c);
+                    console.log("Stripped conflicts:", full);
+                    count++;
+                  }
+                }
+              }
+            }
+            fix(".");
+            console.log(count + " file(s) fixed");
+          '
+
       - name: Setup PNPM
         if: steps.pr.outputs.number != '' && steps.attempts.outputs.skip != 'true'
         uses: pnpm/action-setup@fc06bc1257f339d1d5d8b3a19a8cae5388b55320 # v4.4.0
@@ -102,14 +132,13 @@ jobs:
           node-version: 24.15.0
           cache: pnpm
 
-      - name: Install root deps only
+      - name: Install deps
+        if: steps.pr.outputs.number != '' && steps.attempts.outputs.skip != 'true'
+        run: pnpm install --no-frozen-lockfile
+
+      - name: Build
         if: steps.pr.outputs.number != '' && steps.attempts.outputs.skip != 'true'
-        # Only install root workspace deps (where @flue/cli lives).
-        # Cannot install the full monorepo here because merge conflicts
-        # in package.json files would break pnpm install.
-        # Full install and build happen inside the Flue sandbox after
-        # conflicts are resolved.
-        run: pnpm install --no-frozen-lockfile --filter .
+        run: pnpm build
 
       - name: Log in to GHCR
         if: steps.pr.outputs.number != '' && steps.attempts.outputs.skip != 'true'