@lumenflow/cli 5.5.0 → 5.7.14

package/README.md

@@ -171,46 +171,47 @@ This package provides CLI commands for the LumenFlow workflow framework, includi
 
 ### System & Setup
 
-| Command                    | Description                                                                 |
-| -------------------------- | --------------------------------------------------------------------------- |
-| `backlog-prune`            | Clean stale backlog entries                                                 |
-| `cloud-connect`            | Connect workspace.yaml to cloud control plane                               |
-| `config-get`               | Read and display a value from workspace.yaml software_delivery              |
-| `config-set`               | Safely update workspace.yaml software_delivery via micro-worktree           |
-| `distribution-preflight`   | Audit consumer repos for @lumenflow/\* privatization readiness              |
-| `init-plan`                | Link plan to initiative (alias)                                             |
-| `lumenflow`                | Initialize LumenFlow in a project                                           |
-| `lumenflow-commands`       | List all available CLI commands                                             |
-| `lumenflow-disable`        | Flip enforcement flags to false and regenerate hooks as no-ops (reversible) |
-| `lumenflow-docs-sync`      | Refresh core docs, onboarding docs, and supported vendor assets (alias)     |
-| `lumenflow-doctor`         | Diagnose LumenFlow configuration                                            |
-| `lumenflow-enable`         | Re-enable enforcement after lumenflow:disable (restores prior state)        |
-| `lumenflow-init`           | Initialize LumenFlow in a project (alias)                                   |
-| `lumenflow-integrate`      | Generate enforcement hooks for client                                       |
-| `lumenflow-onboard`        | Legacy entrypoint; use "npx lumenflow" for bootstrap-all onboarding         |
-| `lumenflow-release`        | Run release workflow                                                        |
-| `lumenflow-sync-templates` | Sync templates to project                                                   |
-| `lumenflow-uninstall`      | Remove LumenFlow-generated files (dry-run by default; requires --confirm)   |
-| `lumenflow-upgrade`        | Upgrade LumenFlow packages                                                  |
-| `onboard`                  | Legacy entrypoint; use "npx lumenflow" for bootstrap-all onboarding         |
-| `pack-author`              | Author a secure domain pack from templates                                  |
-| `pack-hash`                | Compute integrity hash for a domain pack                                    |
-| `pack-install`             | Install a domain pack into workspace                                        |
-| `pack-publish`             | Publish a domain pack to a registry                                         |
-| `pack-scaffold`            | Scaffold a new domain pack                                                  |
-| `pack-search`              | Search for domain packs in a registry                                       |
-| `pack-validate`            | Validate a domain pack for integrity                                        |
-| `plan-create`              | Create a new plan                                                           |
-| `plan-edit`                | Edit plan content                                                           |
-| `plan-link`                | Link plan to WU or initiative                                               |
-| `plan-promote`             | Promote plan to WU                                                          |
-| `state-bootstrap`          | Bootstrap state store                                                       |
-| `state-cleanup`            | Clean up stale state data                                                   |
-| `state-doctor`             | Diagnose state store issues                                                 |
-| `state-emit`               | Emit corrective event to state store (WU-2241)                              |
-| `sync-templates`           | Sync templates to project (alias)                                           |
-| `templates-sync`           | Sync templates to project (alias)                                           |
-| `workspace-init`           | Legacy entrypoint; use "npx lumenflow" for bootstrap-all onboarding         |
+| Command                    | Description                                                                                                |
+| -------------------------- | ---------------------------------------------------------------------------------------------------------- |
+| `backlog-prune`            | Clean stale backlog entries                                                                                |
+| `cloud-connect`            | Connect workspace.yaml to cloud control plane                                                              |
+| `config-get`               | Read and display a value from workspace.yaml software_delivery                                             |
+| `config-set`               | Safely update workspace.yaml software_delivery via micro-worktree                                          |
+| `db-journal-recover`       | Detect drizzle journal collisions and offer a safe-resequence path (dry-run by default; --confirm applies) |
+| `init-plan`                | Link plan to initiative (alias)                                                                            |
+| `lumenflow`                | Initialize LumenFlow in a project                                                                          |
+| `lumenflow-commands`       | List all available CLI commands                                                                            |
+| `lumenflow-disable`        | Flip enforcement flags to false and regenerate hooks as no-ops (reversible)                                |
+| `lumenflow-docs-sync`      | Refresh core docs, onboarding docs, and supported vendor assets (alias)                                    |
+| `lumenflow-doctor`         | Diagnose LumenFlow configuration                                                                           |
+| `lumenflow-enable`         | Re-enable enforcement after lumenflow:disable (restores prior state)                                       |
+| `lumenflow-init`           | Initialize LumenFlow in a project (alias)                                                                  |
+| `lumenflow-integrate`      | Generate enforcement hooks for client                                                                      |
+| `lumenflow-onboard`        | Legacy entrypoint; use "npx lumenflow" for bootstrap-all onboarding                                        |
+| `lumenflow-release`        | Run release workflow                                                                                       |
+| `lumenflow-setup-prereqs`  | Surface external prerequisites (e.g. Supabase CLI) at end of pnpm setup                                    |
+| `lumenflow-sync-templates` | Sync templates to project                                                                                  |
+| `lumenflow-uninstall`      | Remove LumenFlow-generated files (dry-run by default; requires --confirm)                                  |
+| `lumenflow-upgrade`        | Upgrade LumenFlow packages                                                                                 |
+| `onboard`                  | Legacy entrypoint; use "npx lumenflow" for bootstrap-all onboarding                                        |
+| `pack-author`              | Author a secure domain pack from templates                                                                 |
+| `pack-hash`                | Compute integrity hash for a domain pack                                                                   |
+| `pack-install`             | Install a domain pack into workspace                                                                       |
+| `pack-publish`             | Publish a domain pack to a registry                                                                        |
+| `pack-scaffold`            | Scaffold a new domain pack                                                                                 |
+| `pack-search`              | Search for domain packs in a registry                                                                      |
+| `pack-validate`            | Validate a domain pack for integrity                                                                       |
+| `plan-create`              | Create a new plan                                                                                          |
+| `plan-edit`                | Edit plan content                                                                                          |
+| `plan-link`                | Link plan to WU or initiative                                                                              |
+| `plan-promote`             | Promote plan to WU                                                                                         |
+| `state-bootstrap`          | Bootstrap state store                                                                                      |
+| `state-cleanup`            | Clean up stale state data                                                                                  |
+| `state-doctor`             | Diagnose state store issues                                                                                |
+| `state-emit`               | Emit corrective event to state store (WU-2241)                                                             |
+| `sync-templates`           | Sync templates to project (alias)                                                                          |
+| `templates-sync`           | Sync templates to project (alias)                                                                          |
+| `workspace-init`           | Legacy entrypoint; use "npx lumenflow" for bootstrap-all onboarding                                        |
 
 ### File & Git Operations
 

package/dist/db-journal-recover.js

@@ -0,0 +1,400 @@
+#!/usr/bin/env node
+// Copyright (c) 2026 Hellmai Ltd
+// SPDX-License-Identifier: LicenseRef-LumenFlow-Proprietary
+/**
+ * @file db-journal-recover.ts
+ * WU-2945: First-class CLI command for drizzle journal collision recovery.
+ *
+ * Background: cloud INIT-105 hit drizzle journal collisions in 4+ WUs where
+ * two snapshots shared the same prevId (chain fork). drizzle-kit generate has
+ * no recovery story; agents resorted to manual journal surgery and skip-gates.
+ * This command surfaces the recovery as a documented, scriptable, idempotent
+ * primitive.
+ *
+ * Detection: parses drizzle/meta/_journal.json + snapshot files. Reports a
+ * collision when two or more snapshots share a prevId OR when journal entries
+ * have duplicate idx values.
+ *
+ * Recovery: re-links snapshots in sorted-idx order so each snapshot's prevId
+ * equals the previous snapshot's id; re-emits journal entries with sequential
+ * idx values. Idempotent: re-running on a healthy chain is a no-op.
+ *
+ * Safety: dry-run is the default. --confirm is required to write to disk.
+ * Every actual rewrite emits an audit log under .lumenflow/db-recovery/.
+ *
+ * Usage:
+ *   pnpm db:journal-recover                  # dry-run (default), prints plan
+ *   pnpm db:journal-recover --confirm        # apply plan, write audit log
+ *   pnpm db:journal-recover --drizzle-dir <path>  # custom drizzle dir
+ *   pnpm db:journal-recover --help
+ */
+import { readFile, writeFile, mkdir, readdir } from 'node:fs/promises';
+import { existsSync } from 'node:fs';
+import path from 'node:path';
+import { findProjectRoot } from '@lumenflow/core/config';
+import { die, createError, ErrorCodes } from '@lumenflow/core/error-handler';
+import { runCLI } from './cli-entry-point.js';
+const LOG_PREFIX = '[db:journal-recover]';
+const ARG_HELP = '--help';
+const ARG_DRY_RUN = '--dry-run';
+const ARG_CONFIRM = '--confirm';
+const ARG_JSON = '--json';
+const ARG_DRIZZLE_DIR = '--drizzle-dir';
+const DEFAULT_DRIZZLE_DIR = 'drizzle';
+const META_DIR = 'meta';
+const JOURNAL_FILENAME = '_journal.json';
+const SNAPSHOT_SUFFIX = '_snapshot.json';
+const AUDIT_LOG_DIR = '.lumenflow/db-recovery';
+const SNAPSHOT_NAME_PATTERN = /^(\d+)_snapshot\.json$/;
+export function parseJournalRecoverArgs(argv) {
+    const help = argv.includes(ARG_HELP);
+    const json = argv.includes(ARG_JSON);
+    // dry-run is default; --confirm switches to write mode.
+    const confirm = argv.includes(ARG_CONFIRM);
+    const dirIdx = argv.indexOf(ARG_DRIZZLE_DIR);
+    const drizzleDir = dirIdx >= 0 && dirIdx + 1 < argv.length ? argv[dirIdx + 1] : DEFAULT_DRIZZLE_DIR;
+    // --dry-run is accepted as an explicit no-op for clarity in scripts.
+    void argv.includes(ARG_DRY_RUN);
+    return { help, json, confirm, drizzleDir };
+}
+export function getJournalRecoverHelpText() {
+    return `Usage: pnpm db:journal-recover [options]
+
+Detect drizzle journal collisions and offer a safe-resequence path.
+
+A collision is two or more snapshots sharing the same prevId (chain fork) or
+journal entries sharing the same idx. Recovery re-links snapshots in sorted-idx
+order so each snapshot's prevId matches the previous snapshot's id, and
+re-emits journal entries with sequential idx values.
+
+Default mode is dry-run (no files modified). Use --confirm to apply the plan;
+an audit log is written under ${AUDIT_LOG_DIR}/<timestamp>.log.
+
+Idempotent: re-running on a healthy chain is a no-op.
+
+Options:
+  ${ARG_DRIZZLE_DIR} <path>   Drizzle directory (default: ${DEFAULT_DRIZZLE_DIR})
+  ${ARG_DRY_RUN}             Show planned resequence without writing (default)
+  ${ARG_CONFIRM}              Apply plan, write files, emit audit log
+  ${ARG_JSON}                 Emit machine-readable JSON instead of text
+  ${ARG_HELP}                 Show this help text and exit
+
+Examples:
+  pnpm db:journal-recover
+  pnpm db:journal-recover --drizzle-dir packages/db/drizzle
+  pnpm db:journal-recover --confirm
+`;
+}
+/**
+ * Parse the numeric idx prefix from a snapshot filename.
+ * Returns null if filename doesn't match the expected pattern.
+ */
+export function parseSnapshotIdx(filename) {
+    const match = SNAPSHOT_NAME_PATTERN.exec(filename);
+    if (!match)
+        return null;
+    return Number.parseInt(match[1], 10);
+}
+/**
+ * Detect collisions in a snapshot/journal pair.
+ * Pure function: takes parsed inputs, returns a CollisionReport.
+ */
+export function detectCollisions(snapshots, journal) {
+    const prevIdGroups = new Map();
+    const snapshotIdxGroups = new Map();
+    for (const snap of snapshots) {
+        const list = prevIdGroups.get(snap.doc.prevId) ?? [];
+        list.push(snap.filename);
+        prevIdGroups.set(snap.doc.prevId, list);
+        const idxList = snapshotIdxGroups.get(snap.idx) ?? [];
+        idxList.push(snap.filename);
+        snapshotIdxGroups.set(snap.idx, idxList);
+    }
+    const duplicatePrevIds = [];
+    for (const [prevId, filenames] of prevIdGroups) {
+        if (filenames.length > 1)
+            duplicatePrevIds.push({ prevId, filenames });
+    }
+    const duplicateSnapshotIdx = [];
+    for (const [idx, filenames] of snapshotIdxGroups) {
+        if (filenames.length > 1)
+            duplicateSnapshotIdx.push({ idx, filenames });
+    }
+    const duplicateIdx = [];
+    if (journal) {
+        const journalIdxGroups = new Map();
+        for (const entry of journal.entries) {
+            const tags = journalIdxGroups.get(entry.idx) ?? [];
+            tags.push(entry.tag);
+            journalIdxGroups.set(entry.idx, tags);
+        }
+        for (const [idx, tags] of journalIdxGroups) {
+            if (tags.length > 1)
+                duplicateIdx.push({ idx, tags });
+        }
+    }
+    return { duplicatePrevIds, duplicateIdx, duplicateSnapshotIdx };
+}
+/**
+ * Build a recovery plan from snapshots + journal.
+ *
+ * Strategy: sort snapshots by numeric idx, then re-link prevId so each
+ * snapshot's prevId equals the previous snapshot's id (or the canonical
+ * empty-uuid for idx=0 if no first prevId is set). The first snapshot's
+ * prevId is preserved (it points at drizzle's initial empty-uuid sentinel).
+ */
+export function buildRecoveryPlan(snapshots, journal) {
+    const collisions = detectCollisions(snapshots, journal);
+    const sorted = [...snapshots].sort((a, b) => a.idx - b.idx);
+    const steps = [];
+    let previousId = null;
+    for (const snap of sorted) {
+        const prevIdBefore = snap.doc.prevId;
+        // First snapshot keeps its existing prevId (drizzle's empty-uuid sentinel).
+        const prevIdAfter = previousId === null ? prevIdBefore : previousId;
+        steps.push({
+            filename: snap.filename,
+            idx: snap.idx,
+            prevIdBefore,
+            prevIdAfter,
+            changed: prevIdBefore !== prevIdAfter,
+        });
+        previousId = snap.doc.id;
+    }
+    const journalRewriteRequired = collisions.duplicateIdx.length > 0 ||
+        (journal !== null && needsJournalResequence(journal, sorted));
+    const alreadyHealthy = collisions.duplicatePrevIds.length === 0 &&
+        collisions.duplicateIdx.length === 0 &&
+        collisions.duplicateSnapshotIdx.length === 0 &&
+        steps.every((s) => !s.changed) &&
+        !journalRewriteRequired;
+    return { collisions, steps, journalRewriteRequired, alreadyHealthy };
+}
+function needsJournalResequence(journal, sorted) {
+    if (journal.entries.length !== sorted.length)
+        return true;
+    for (let i = 0; i < sorted.length; i++) {
+        if (journal.entries[i].idx !== i)
+            return true;
+    }
+    return false;
+}
+/**
+ * Re-emit the journal with sequential idx values (0..n-1) preserving the
+ * existing tag order matched against the sorted snapshots by tag prefix.
+ */
+export function resequenceJournal(journal, sorted) {
+    // Map snapshot filename prefix (e.g. '0023') to journal entry by tag prefix.
+    const taggedByPrefix = new Map();
+    for (const entry of journal.entries) {
+        const prefix = entry.tag.split('_')[0];
+        taggedByPrefix.set(prefix, entry);
+    }
+    const newEntries = sorted.map((snap, idx) => {
+        const prefix = snap.filename.split('_')[0];
+        const original = taggedByPrefix.get(prefix);
+        if (!original) {
+            throw createError(ErrorCodes.VALIDATION_ERROR, `${LOG_PREFIX} Cannot rebuild journal: snapshot ${snap.filename} has no matching journal entry. ` +
+                `Run drizzle-kit generate to regenerate the journal, then retry.`, { filename: snap.filename });
+        }
+        return { ...original, idx };
+    });
+    return { ...journal, entries: newEntries };
+}
+/**
+ * Format a recovery plan as a human-readable string.
+ */
+export function formatPlan(plan, drizzleDirRel) {
+    const lines = [];
+    lines.push(`${LOG_PREFIX} Drizzle directory: ${drizzleDirRel}`);
+    if (plan.alreadyHealthy) {
+        lines.push(`${LOG_PREFIX} ✅ Journal is healthy. Nothing to do.`);
+        return lines.join('\n');
+    }
+    if (plan.collisions.duplicatePrevIds.length > 0) {
+        lines.push('');
+        lines.push('Collisions: snapshots sharing the same prevId:');
+        for (const entry of plan.collisions.duplicatePrevIds) {
+            lines.push(`  prevId=${entry.prevId}`);
+            for (const file of entry.filenames)
+                lines.push(`    - ${file}`);
+        }
+    }
+    if (plan.collisions.duplicateIdx.length > 0) {
+        lines.push('');
+        lines.push('Collisions: journal entries with duplicate idx:');
+        for (const entry of plan.collisions.duplicateIdx) {
+            lines.push(`  idx=${entry.idx} tags=${entry.tags.join(', ')}`);
+        }
+    }
+    if (plan.collisions.duplicateSnapshotIdx.length > 0) {
+        lines.push('');
+        lines.push('Collisions: snapshot files with duplicate numeric idx:');
+        for (const entry of plan.collisions.duplicateSnapshotIdx) {
+            lines.push(`  idx=${entry.idx}`);
+            for (const file of entry.filenames)
+                lines.push(`    - ${file}`);
+        }
+    }
+    const changed = plan.steps.filter((s) => s.changed);
+    if (changed.length > 0) {
+        lines.push('');
+        lines.push('Planned snapshot prevId rewrites:');
+        for (const step of changed) {
+            lines.push(`  ${step.filename}: ${step.prevIdBefore} -> ${step.prevIdAfter}`);
+        }
+    }
+    if (plan.journalRewriteRequired) {
+        lines.push('');
+        lines.push(`Planned journal rewrite: idx values will be resequenced 0..${plan.steps.length - 1}`);
+    }
+    lines.push('');
+    lines.push('Run with --confirm to apply. Audit log will be written to');
+    lines.push(`  ${AUDIT_LOG_DIR}/<timestamp>.log`);
+    return lines.join('\n');
+}
+/**
+ * Read snapshot files from the drizzle meta directory.
+ */
+export async function loadSnapshots(metaDir) {
+    if (!existsSync(metaDir))
+        return [];
+    const entries = await readdir(metaDir);
+    const snapshotFiles = entries.filter((e) => e.endsWith(SNAPSHOT_SUFFIX));
+    const result = [];
+    for (const filename of snapshotFiles) {
+        const idx = parseSnapshotIdx(filename);
+        if (idx === null)
+            continue;
+        const raw = await readFile(path.join(metaDir, filename), 'utf8');
+        const doc = JSON.parse(raw);
+        if (typeof doc.id !== 'string' || typeof doc.prevId !== 'string') {
+            throw createError(ErrorCodes.VALIDATION_ERROR, `${LOG_PREFIX} ${filename} is missing id/prevId fields. ` +
+                `Expected drizzle snapshot shape; got: ${Object.keys(doc).join(', ')}`, { filename, keys: Object.keys(doc) });
+        }
+        result.push({ filename, idx, doc });
+    }
+    return result;
+}
+/**
+ * Read the journal file from the drizzle meta directory.
+ */
+export async function loadJournal(metaDir) {
+    const journalPath = path.join(metaDir, JOURNAL_FILENAME);
+    if (!existsSync(journalPath))
+        return null;
+    const raw = await readFile(journalPath, 'utf8');
+    return JSON.parse(raw);
+}
+/**
+ * Apply a recovery plan to disk. Idempotent: if the plan changes nothing,
+ * no files are touched and no audit log is written.
+ *
+ * Returns the list of files that were written.
+ */
+export async function applyRecoveryPlan(params) {
+    const { metaDir, snapshots, journal, plan, auditDir, now } = params;
+    if (plan.alreadyHealthy)
+        return [];
+    const written = [];
+    // Rewrite snapshots that need their prevId updated.
+    const snapByFilename = new Map(snapshots.map((s) => [s.filename, s]));
+    for (const step of plan.steps) {
+        if (!step.changed)
+            continue;
+        const snap = snapByFilename.get(step.filename);
+        if (!snap)
+            continue;
+        const newDoc = { ...snap.doc, prevId: step.prevIdAfter };
+        const filePath = path.join(metaDir, step.filename);
+        await writeFile(filePath, `${JSON.stringify(newDoc, null, 2)}\n`, 'utf8');
+        written.push(filePath);
+    }
+    // Resequence journal if needed.
+    if (plan.journalRewriteRequired && journal) {
+        const sorted = [...snapshots].sort((a, b) => a.idx - b.idx);
+        const newJournal = resequenceJournal(journal, sorted);
+        const journalPath = path.join(metaDir, JOURNAL_FILENAME);
+        await writeFile(journalPath, `${JSON.stringify(newJournal, null, 2)}\n`, 'utf8');
+        written.push(journalPath);
+    }
+    // Audit log.
+    const timestamp = (now ? now() : new Date()).toISOString().replace(/[:.]/g, '-');
+    await mkdir(auditDir, { recursive: true });
+    const auditPath = path.join(auditDir, `${timestamp}.log`);
+    await writeFile(auditPath, formatAuditLog(plan, written), 'utf8');
+    written.push(auditPath);
+    return written;
+}
+export function formatAuditLog(plan, writtenFiles) {
+    const lines = [];
+    lines.push(`db:journal-recover audit log`);
+    lines.push(`generated: ${new Date().toISOString()}`);
+    lines.push('');
+    lines.push('Collisions detected:');
+    lines.push(`  duplicatePrevIds: ${plan.collisions.duplicatePrevIds.length}`);
+    lines.push(`  duplicateIdx: ${plan.collisions.duplicateIdx.length}`);
+    lines.push(`  duplicateSnapshotIdx: ${plan.collisions.duplicateSnapshotIdx.length}`);
+    lines.push('');
+    lines.push('Steps:');
+    for (const step of plan.steps) {
+        if (!step.changed)
+            continue;
+        lines.push(`  ${step.filename}: prevId ${step.prevIdBefore} -> ${step.prevIdAfter}`);
+    }
+    if (plan.journalRewriteRequired) {
+        lines.push('  journal: idx resequenced');
+    }
+    lines.push('');
+    lines.push('Files written:');
+    for (const file of writtenFiles)
+        lines.push(`  ${file}`);
+    return `${lines.join('\n')}\n`;
+}
+async function main() {
+    const args = parseJournalRecoverArgs(process.argv.slice(2));
+    if (args.help) {
+        console.log(getJournalRecoverHelpText());
+        return;
+    }
+    const projectRoot = findProjectRoot();
+    const drizzleDirAbs = path.isAbsolute(args.drizzleDir)
+        ? args.drizzleDir
+        : path.join(projectRoot, args.drizzleDir);
+    const metaDir = path.join(drizzleDirAbs, META_DIR);
+    if (!existsSync(metaDir)) {
+        die(`${LOG_PREFIX} No drizzle meta directory at ${metaDir}.\n\n` +
+            `Expected ${args.drizzleDir}/${META_DIR}/${JOURNAL_FILENAME}. ` +
+            `Pass ${ARG_DRIZZLE_DIR} <path> if your drizzle output lives elsewhere.`);
+    }
+    const snapshots = await loadSnapshots(metaDir);
+    const journal = await loadJournal(metaDir);
+    const plan = buildRecoveryPlan(snapshots, journal);
+    if (args.json) {
+        console.log(JSON.stringify(plan, null, 2));
+    }
+    else {
+        const drizzleDirRel = path.relative(projectRoot, drizzleDirAbs) || args.drizzleDir;
+        console.log(formatPlan(plan, drizzleDirRel));
+    }
+    if (!args.confirm)
+        return;
+    if (plan.alreadyHealthy)
+        return;
+    const auditDir = path.join(projectRoot, AUDIT_LOG_DIR);
+    const written = await applyRecoveryPlan({
+        metaDir,
+        snapshots,
+        journal,
+        plan,
+        auditDir,
+    });
+    console.log('');
+    console.log(`${LOG_PREFIX} ✅ Wrote ${written.length} file(s):`);
+    for (const file of written)
+        console.log(`  ${path.relative(projectRoot, file)}`);
+}
+if (import.meta.main) {
+    void runCLI(main);
+}
+//# sourceMappingURL=db-journal-recover.js.map

package/dist/db-journal-recover.js.map

@@ -0,0 +1 @@
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package/dist/docs-sync.js

@@ -337,11 +337,16 @@ const SKILL_TEMPLATE_PATHS = {
  * User-created skills outside this list are never touched.
  */
 export const RESERVED_SKILL_NAMES = Object.keys(SKILL_TEMPLATE_PATHS);
+function unwrapBootstrapBlockContent(processedContent) {
+    const extraction = extractMergeBlock(processedContent);
+    return extraction.found ? (extraction.content ?? '') : processedContent;
+}
 function mergeBootstrapContent(filePath, processedContent, targetDir, result) {
     const relativePath = path.relative(targetDir, filePath).split(path.sep).join('/');
+    const blockContent = unwrapBootstrapBlockContent(processedContent);
     if (fs.existsSync(filePath)) {
         const existingContent = fs.readFileSync(filePath, 'utf-8');
-        const migratedLegacyContent = migrateLegacyBootstrapScaffold(existingContent, processedContent);
+        const migratedLegacyContent = migrateLegacyBootstrapScaffold(existingContent, blockContent);
         if (migratedLegacyContent !== null) {
             if (migratedLegacyContent === existingContent) {
                 result.skipped.push(relativePath);
@@ -352,7 +357,7 @@ function mergeBootstrapContent(filePath, processedContent, targetDir, result) {
             }
             return;
         }
-        const mergeResult = updateMergeBlock(existingContent, processedContent);
+        const mergeResult = updateMergeBlock(existingContent, blockContent);
         if (mergeResult.updated) {
             fs.writeFileSync(filePath, mergeResult.content);
             result.created.push(relativePath);
@@ -366,7 +371,7 @@ function mergeBootstrapContent(filePath, processedContent, targetDir, result) {
         }
         return;
     }
-    const wrappedContent = `${MARKERS.START}\n${processedContent}\n${MARKERS.END}\n`;
+    const wrappedContent = `${MARKERS.START}\n${blockContent}\n${MARKERS.END}\n`;
     const parentDir = path.dirname(filePath);
     if (!fs.existsSync(parentDir)) {
         fs.mkdirSync(parentDir, { recursive: true });