@blxzer/cursor-trellis 0.3.0 → 0.3.3

package/dist/commands/uninstall.js

@@ -1,9 +1,9 @@
 /**
  * `cstl uninstall` — remove every file written by `cstl init` / `update`
- * from the current project, plus the `.trellis/` directory itself.
+ * from the current project, plus the `.cstl/` directory itself.
  *
  * The single source of truth for "what trellis wrote" is
- * `.trellis/.template-hashes.json`. Files outside that manifest are never
+ * `.cstl/.template-hashes.json`. Files outside that manifest are never
  * touched (e.g. user-added hooks under `.cursor/hooks/`).
  *
  * Manifest-listed files split into two groups:
@@ -14,18 +14,19 @@
  *      file is fully empty afterwards, we delete it.
  *
  * Whether the user has modified a manifest-listed file or not, it is removed
- * (per the PRD: "全删"). The `.trellis/` tree is removed unconditionally.
+ * (per the PRD: "全删"). The `.cstl/` tree is removed unconditionally.
  */
 import fs from "node:fs";
 import path from "node:path";
 import readline from "node:readline";
 import chalk from "chalk";
 import inquirer from "inquirer";
-import { DIR_NAMES } from "../constants/paths.js";
+import { DIR_NAMES, FILE_NAMES } from "../constants/paths.js";
 import { loadHashes } from "../utils/template-hash.js";
 import { cleanupEmptyDirs } from "./update.js";
 import { ALL_MANAGED_DIRS, getConfiguredPlatforms, } from "../configurators/index.js";
 import { pruneOrphanManifestKeys } from "../utils/manifest-prune.js";
+import { hasCstlBlock, removeCstlManagedBlock, } from "../utils/agents-md.js";
 import { isCwdHomedir, homedirGuardMessage, homedirBypassEnabled, } from "../utils/cwd-guard.js";
 import { scrubHooksJson } from "../utils/uninstall-scrubbers.js";
 /**
@@ -47,6 +48,25 @@ function buildStructuredFileSpecs() {
     }
     return map;
 }
+/**
+ * Decide the uninstall action for the root `AGENTS.md`. Independent of the
+ * manifest because AGENTS.md is pruned from it (see `pruneOrphanManifestKeys`).
+ */
+function planAgentsMdAction(cwd) {
+    const absPath = path.join(cwd, FILE_NAMES.AGENTS);
+    if (!fs.existsSync(absPath)) {
+        return { kind: "none" };
+    }
+    const content = fs.readFileSync(absPath, "utf-8");
+    if (!hasCstlBlock(content)) {
+        return { kind: "none" };
+    }
+    const stripped = removeCstlManagedBlock(content);
+    if (stripped.trim() === "") {
+        return { kind: "delete", absPath };
+    }
+    return { kind: "strip", absPath, strippedContent: stripped };
+}
 /**
  * Walk through the manifest and decide, for each entry, whether it is a plain
  * deletion or a structured modification (or fully-empty modification → still
@@ -58,6 +78,13 @@ function buildPlan(cwd, hashes) {
     const deletions = [];
     const modifications = [];
     for (const posixPath of allPosixPaths) {
+        // AGENTS.md is handled by `plan.agentsMd` (strip CSTL block, preserve any
+        // upstream TRELLIS block + user content). Skip it here so the manifest
+        // loop never deletes the whole file — that would drop the upstream block
+        // and user content in a coexistence repo.
+        if (posixPath === FILE_NAMES.AGENTS) {
+            continue;
+        }
         const absPath = path.join(cwd, ...posixPath.split("/"));
         const spec = structured.get(posixPath);
         if (!spec) {
@@ -92,6 +119,7 @@ function buildPlan(cwd, hashes) {
         deletions,
         modifications,
         removeTrellisDir: true,
+        agentsMd: planAgentsMdAction(cwd),
     };
 }
 /**
@@ -103,19 +131,30 @@ function renderPlan(cwd, plan) {
     const deletePaths = plan.deletions
         .filter((d) => !d.missing)
         .map((d) => d.posixPath);
-    console.log(chalk.red.bold(`Will be deleted (${deletePaths.length + 1} entries):`));
+    const agentsDelete = plan.agentsMd.kind === "delete";
+    const cstlDirShown = plan.removeTrellisDir && fs.existsSync(trellisDir);
+    const deleteCount = deletePaths.length + (cstlDirShown ? 1 : 0) + (agentsDelete ? 1 : 0);
+    console.log(chalk.red.bold(`Will be deleted (${deleteCount} entries):`));
     for (const p of deletePaths) {
         console.log(`  ${chalk.red("-")} ${p}`);
     }
-    if (plan.removeTrellisDir && fs.existsSync(trellisDir)) {
+    if (agentsDelete) {
+        console.log(`  ${chalk.red("-")} ${FILE_NAMES.AGENTS}  ${chalk.gray("(only the cursor-trellis managed block was present)")}`);
+    }
+    if (cstlDirShown) {
         console.log(`  ${chalk.red("-")} ${DIR_NAMES.WORKFLOW}/  ${chalk.gray("(entire directory, including tasks/runtime/config)")}`);
     }
-    if (plan.modifications.length > 0) {
+    const agentsStrip = plan.agentsMd.kind === "strip";
+    const modCount = plan.modifications.length + (agentsStrip ? 1 : 0);
+    if (modCount > 0) {
         console.log();
-        console.log(chalk.yellow.bold(`Will be modified (${plan.modifications.length} files):`));
+        console.log(chalk.yellow.bold(`Will be modified (${modCount} files):`));
         for (const m of plan.modifications) {
             console.log(`  ${chalk.yellow("~")} ${m.posixPath}  ${chalk.gray(`(${m.reason})`)}`);
         }
+        if (agentsStrip) {
+            console.log(`  ${chalk.yellow("~")} ${FILE_NAMES.AGENTS}  ${chalk.gray("(strip cursor-trellis managed block; keep upstream + user content)")}`);
+        }
     }
     const skipped = plan.deletions.filter((d) => d.missing);
     if (skipped.length > 0) {
@@ -142,7 +181,7 @@ async function promptContinue() {
     return proceed;
 }
 /**
- * Execute the plan: write modifications, unlink deletions, remove `.trellis/`,
+ * Execute the plan: write modifications, unlink deletions, remove `.cstl/`,
  * then prune empty managed directories.
  *
  * Returns counts for the summary.
@@ -155,6 +194,21 @@ function executePlan(cwd, plan) {
         fs.writeFileSync(mod.absPath, mod.result.content);
         modifiedFiles += 1;
     }
+    // 1b. AGENTS.md CSTL-block strip (or delete if only the block was present).
+    // Handled outside the manifest loop because AGENTS.md is pruned from it.
+    if (plan.agentsMd.kind === "strip") {
+        fs.writeFileSync(plan.agentsMd.absPath, plan.agentsMd.strippedContent);
+        modifiedFiles += 1;
+    }
+    else if (plan.agentsMd.kind === "delete") {
+        try {
+            fs.unlinkSync(plan.agentsMd.absPath);
+            deletedFiles += 1;
+        }
+        catch {
+            // Best-effort; a missing/locked file is reported via summary mismatch.
+        }
+    }
     // 2. Deletions (skip already-missing entries).
     const deletedDirCandidates = new Set();
     for (const del of plan.deletions) {
@@ -172,7 +226,7 @@ function executePlan(cwd, plan) {
         }
         deletedDirCandidates.add(path.posix.dirname(del.posixPath));
     }
-    // 3. Drop `.trellis/` entirely.
+    // 3. Drop `.cstl/` entirely.
     let deletedDirs = 0;
     if (plan.removeTrellisDir) {
         const trellisDir = path.join(cwd, DIR_NAMES.WORKFLOW);
@@ -194,7 +248,7 @@ function executePlan(cwd, plan) {
     // `.agents/skills`, …) that is now empty. We deliberately handle this here
     // — `cleanupEmptyDirs` refuses to touch managed root dirs because in normal
     // `update` flow they must persist. During uninstall, an empty platform root
-    // has no purpose. `.trellis` is already gone (step 3), so we skip it.
+    // has no purpose. `.cstl` is already gone (step 3), so we skip it.
     // Process deepest-first so that nested managed dirs (e.g. `.agents/skills`)
     // are removed before their parents (`.agents`).
     const sortedManagedDirs = [...ALL_MANAGED_DIRS]
@@ -247,9 +301,9 @@ export async function uninstall(options = {}) {
     }
     const cwd = process.cwd();
     const trellisDir = path.join(cwd, DIR_NAMES.WORKFLOW);
-    // Pre-check 1: must have a `.trellis/` directory.
+    // Pre-check 1: must have a `.cstl/` directory.
     if (!fs.existsSync(trellisDir)) {
-        console.log(chalk.gray("Trellis is not installed in this project (no .trellis/ directory found)."));
+        console.log(chalk.gray("Trellis is not installed in this project (no .cstl/ directory found)."));
         return;
     }
     // Pre-check 2: must have a manifest. Without it we cannot determine which
@@ -257,7 +311,7 @@ export async function uninstall(options = {}) {
     const hashes = loadHashes(cwd);
     if (Object.keys(hashes).length === 0) {
         console.error(chalk.red("Trellis directory found but manifest is missing — cannot determine which platform files to remove. " +
-            "You can manually delete .trellis/ if needed."));
+            "You can manually delete .cstl/ if needed."));
         process.exit(1);
     }
     // Self-heal poisoned manifests from buggy init versions: prune any manifest
@@ -268,7 +322,7 @@ export async function uninstall(options = {}) {
     // Dry-run: still compute the pruned hashes (so the plan reflects post-prune
     // reality) but pass `persist: false` so no disk write happens. The actual
     // disk write defers to executePlan time, where we'd be rewriting the
-    // manifest only to delete the whole .trellis/ dir anyway — but the
+    // manifest only to delete the whole .cstl/ dir anyway — but the
     // computation must remain to keep the rendered plan honest.
     const configuredPlatforms = getConfiguredPlatforms(cwd);
     const { pruned, hashes: prunedHashes } = pruneOrphanManifestKeys(cwd, [...configuredPlatforms], hashes, { persist: !options.dryRun });

package/dist/commands/uninstall.js.map

@@ -1 +1 @@
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package/dist/commands/update.d.ts

@@ -12,11 +12,16 @@ export interface UpdateOptions {
     json?: boolean;
     /** Skip post-apply Python script smoke checks (apply mode only). */
     skipPostUpdateSmoke?: boolean;
+    /**
+     * F5 escape hatch: force the `.trellis/` → `.cstl/` rename-dir migration
+     * even when upstream Trellis signals are detected. Requires `--migrate`.
+     */
+    forceCstlMigrate?: boolean;
     /** Filled on completion for `cstl rollout` aggregation. */
     lastReport?: UpdateRolloutReport;
 }
 /**
- * Load update.skip paths from .trellis/config.yaml
+ * Load update.skip paths from .cstl/config.yaml
  *
  * Parses simple YAML structure:
  *   update:

package/dist/commands/update.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../src/commands/update.ts"],"names":[],"mappings":"AAcA,OAAO,KAAK,EACV,kBAAkB,EAClB,aAAa,EAKd,MAAM,uBAAuB,CAAC;AA2D/B,OAAO,EAQL,KAAK,mBAAmB,EACzB,MAAM,mCAAmC,CAAC;AAe3C,MAAM,WAAW,aAAa;IAC5B,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,0EAA0E;IAC1E,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,oEAAoE;IACpE,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B;;;OAGG;IACH,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,2DAA2D;IAC3D,UAAU,CAAC,EAAE,mBAAmB,CAAC;CAClC;AA4ZD;;;;;;;;;;GAUG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CA6DzD;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,oBAAoB,CAClC,QAAQ,EAAE,MAAM,EAChB,cAAc,EAAE,MAAM,GACrB,MAAM,GAAG,IAAI,CA2Bf;AAED;;;;;;;;;GASG;AACH,wBAAgB,wBAAwB,CACtC,OAAO,EAAE,kBAAkB,EAAE,EAC7B,GAAG,EAAE,MAAM,EACX,gBAAgB,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GACpC;IAAE,QAAQ,EAAE,MAAM,CAAA;CAAE,CA0CtB;AAyYD;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAerE;AAsbD;;;GAGG;AACH,0CAA0C;AAC1C,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAgCnE;AAED;;;;GAIG;AACH,0CAA0C;AAC1C,wBAAgB,0BAA0B,CACxC,UAAU,EAAE,aAAa,EAAE,GAC1B,aAAa,EAAE,CAajB;AA2QD;;GAEG;AACH,wBAAsB,MAAM,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CA+gClE"}

package/dist/commands/update.js

@@ -5,6 +5,8 @@ import inquirer from "inquirer";
 import { DIR_NAMES, FILE_NAMES, PATHS } from "../constants/paths.js";
 import { VERSION, PACKAGE_NAME } from "../constants/version.js";
 import { getMigrationsForVersion, getAllMigrations, getMigrationMetadata, getConfigSectionsAddedBetween, } from "../migrations/index.js";
+import { assessCstlDirectoryMigrate } from "../utils/workflow-ownership.js";
+import { isWorkflowInitialized, resolveWorkflowDirName, workflowPath, } from "../utils/workflow-dir.js";
 import { loadHashes, saveHashes, updateHashes, isTemplateModified, removeHash, renameHash, computeHash, } from "../utils/template-hash.js";
 import { compareVersions } from "../utils/compare-versions.js";
 import { toPosix } from "../utils/posix.js";
@@ -30,15 +32,13 @@ function logCursor2plusCompatHint(cwd) {
     if (!fs.existsSync(bundleDir)) {
         return;
     }
-    console.log(chalk.gray("\nCursor++ BYOK: after Cursor/Cursor++ upgrades, run `python .trellis/local/cursor2plus/patch_wpelc8.py --check-compat` before re-applying Method 2.5."));
+    console.log(chalk.gray("\nCursor++ BYOK: after Cursor/Cursor++ upgrades, run `python .cstl/local/cursor2plus/patch_wpelc8.py --check-compat` before re-applying Method 2.5."));
 }
-const TRELLIS_BLOCK_START = "<!-- TRELLIS:START -->";
-const TRELLIS_BLOCK_END = "<!-- TRELLIS:END -->";
+const CSTL_BLOCK_START = "<!-- CSTL:START -->";
+const CSTL_BLOCK_END = "<!-- CSTL:END -->";
+const LEGACY_TRELLIS_BLOCK_START = "<!-- TRELLIS:START -->";
+const LEGACY_TRELLIS_BLOCK_END = "<!-- TRELLIS:END -->";
 const LEGACY_UNTRACKED_AGENTS_MD_BLOCK_HASHES = new Set([
-    // v0.5.0-beta.17 and earlier wrote AGENTS.md but did not hash-track it.
-    // This hash is the pristine Trellis-managed block before the Subagents
-    // section was added, so old untouched projects can be updated without a
-    // false "modified by you" conflict.
     "c1f511b1cfc1902f2147da159f09cc51f380b0c9e341cdb3ac5dea5233f3e307",
 ]);
 // Paths that should never be touched (true user data)
@@ -50,23 +50,37 @@ const PROTECTED_PATHS = [
     `${DIR_NAMES.WORKFLOW}/.developer`,
     `${DIR_NAMES.WORKFLOW}/.current-task`,
 ];
+function getAgentsBlockMarkers(content) {
+    if (content.includes(CSTL_BLOCK_START)) {
+        return { start: CSTL_BLOCK_START, end: CSTL_BLOCK_END };
+    }
+    if (content.includes(LEGACY_TRELLIS_BLOCK_START)) {
+        return {
+            start: LEGACY_TRELLIS_BLOCK_START,
+            end: LEGACY_TRELLIS_BLOCK_END,
+        };
+    }
+    return null;
+}
 function getTrellisManagedBlock(content) {
-    const start = content.indexOf(TRELLIS_BLOCK_START);
-    if (start === -1) {
+    const markers = getAgentsBlockMarkers(content);
+    if (!markers) {
         return null;
     }
-    const end = content.indexOf(TRELLIS_BLOCK_END, start);
+    const start = content.indexOf(markers.start);
+    const end = content.indexOf(markers.end, start);
     if (end === -1) {
         return null;
     }
-    return content.slice(start, end + TRELLIS_BLOCK_END.length);
+    return content.slice(start, end + markers.end.length);
 }
 function replaceTrellisManagedBlock(existingContent, templateContent) {
-    const existingStart = existingContent.indexOf(TRELLIS_BLOCK_START);
-    if (existingStart === -1) {
+    const existingMarkers = getAgentsBlockMarkers(existingContent);
+    if (!existingMarkers) {
         return null;
     }
-    const existingEnd = existingContent.indexOf(TRELLIS_BLOCK_END, existingStart);
+    const existingStart = existingContent.indexOf(existingMarkers.start);
+    const existingEnd = existingContent.indexOf(existingMarkers.end, existingStart);
     if (existingEnd === -1) {
         return null;
     }
@@ -76,7 +90,28 @@ function replaceTrellisManagedBlock(existingContent, templateContent) {
     }
     return (existingContent.slice(0, existingStart) +
         templateBlock +
-        existingContent.slice(existingEnd + TRELLIS_BLOCK_END.length));
+        existingContent.slice(existingEnd + existingMarkers.end.length));
+}
+function includesCstlRuntimeDirRename(migrations) {
+    return migrations.some((item) => item.type === "rename-dir" &&
+        item.from === ".trellis" &&
+        item.to === ".cstl");
+}
+function upgradeAgentsMdToCstlMarkers(cwd) {
+    const agentsPath = path.join(cwd, FILE_NAMES.AGENTS);
+    if (!fs.existsSync(agentsPath)) {
+        return;
+    }
+    const content = fs.readFileSync(agentsPath, "utf-8");
+    if (!content.includes(LEGACY_TRELLIS_BLOCK_START)) {
+        return;
+    }
+    const upgraded = content
+        .replace(LEGACY_TRELLIS_BLOCK_START, CSTL_BLOCK_START)
+        .replace(LEGACY_TRELLIS_BLOCK_END, CSTL_BLOCK_END)
+        .replace(/\.\/\.trellis\//g, "./.cstl/")
+        .replace(/(?<![A-Za-z0-9_])\.trellis\//g, ".cstl/");
+    fs.writeFileSync(agentsPath, upgraded, "utf-8");
 }
 function buildAgentsMdTemplate(cwd) {
     const fullPath = path.join(cwd, FILE_NAMES.AGENTS);
@@ -289,7 +324,7 @@ function executeSafeFileDeletes(classified, cwd) {
     return deleted;
 }
 /**
- * Load update.skip paths from .trellis/config.yaml
+ * Load update.skip paths from .cstl/config.yaml
  *
  * Parses simple YAML structure:
  *   update:
@@ -300,8 +335,8 @@ function executeSafeFileDeletes(classified, cwd) {
  * @internal Exported for testing only
  */
 export function loadUpdateSkipPaths(cwd) {
-    const configPath = path.join(cwd, DIR_NAMES.WORKFLOW, "config.yaml");
-    if (!fs.existsSync(configPath))
+    const configPath = workflowPath(cwd, "config.yaml");
+    if (!configPath || !fs.existsSync(configPath))
         return [];
     try {
         const content = fs.readFileSync(configPath, "utf-8");
@@ -715,7 +750,9 @@ async function promptConflictResolution(file, options, applyToAll) {
  */
 function createBackupDirPath(cwd) {
     const timestamp = new Date().toISOString().replace(/[:.]/g, "-").slice(0, 19);
-    return path.join(cwd, DIR_NAMES.WORKFLOW, `.backup-${timestamp}`);
+    const workflowRoot = workflowPath(cwd, `.backup-${timestamp}`) ??
+        path.join(cwd, DIR_NAMES.WORKFLOW, `.backup-${timestamp}`);
+    return workflowRoot;
 }
 /**
  * Backup a single file to the backup directory
@@ -817,15 +854,16 @@ function createFullBackup(cwd) {
  * Update version file
  */
 function updateVersionFile(cwd) {
-    const versionPath = path.join(cwd, DIR_NAMES.WORKFLOW, ".version");
+    const dirName = resolveWorkflowDirName(cwd) ?? DIR_NAMES.WORKFLOW;
+    const versionPath = path.join(cwd, dirName, ".version");
     fs.writeFileSync(versionPath, VERSION);
 }
 /**
  * Get current installed version
  */
 function getInstalledVersion(cwd) {
-    const versionPath = path.join(cwd, DIR_NAMES.WORKFLOW, ".version");
-    if (fs.existsSync(versionPath)) {
+    const versionPath = workflowPath(cwd, ".version");
+    if (versionPath && fs.existsSync(versionPath)) {
         return fs.readFileSync(versionPath, "utf-8").trim();
     }
     return "unknown";
@@ -957,7 +995,7 @@ function classifyMigrations(migrations, cwd, hashes, templates) {
             continue;
         }
         // For non-rename types, also block writing TO protected paths
-        // rename/rename-dir are allowed to target protected paths (e.g., 0.2.0 renames into .trellis/workspace)
+        // rename/rename-dir are allowed to target protected paths (e.g., 0.2.0 renames into .cstl/workspace)
         if (item.to &&
             isProtectedPath(item.to) &&
             item.type !== "rename" &&
@@ -1310,7 +1348,7 @@ async function executeMigrations(classified, cwd, options) {
         }
         // For `backup-rename`, leave an inline .backup copy of the user's modified
         // original next to the new location (for rename) or in place (for delete).
-        // This is in addition to the full project snapshot at .trellis/.backup-*/;
+        // This is in addition to the full project snapshot at .cstl/.backup-*/;
         // the inline copy is more discoverable when the user wants to diff or merge
         // their customizations against the new template.
         if (item.type === "rename" && item.to) {
@@ -1335,7 +1373,7 @@ async function executeMigrations(classified, cwd, options) {
             const filePath = path.join(cwd, item.from);
             if (action === "backup-rename") {
                 // Keep a .backup copy in place before deletion so the user can recover
-                // inline without digging through .trellis/.backup-*/.
+                // inline without digging through .cstl/.backup-*/.
                 fs.copyFileSync(filePath, filePath + ".backup");
             }
             fs.unlinkSync(filePath);
@@ -1472,8 +1510,8 @@ export async function update(options) {
         });
         finishRollout(options, report);
     };
-    // Check if Trellis is initialized
-    if (!fs.existsSync(path.join(cwd, DIR_NAMES.WORKFLOW))) {
+    // Check if cursor-trellis is initialized (.cstl/ or legacy .trellis/)
+    if (!isWorkflowInitialized(cwd)) {
         console.log(chalk.red("Error: Trellis not initialized in this directory."));
         console.log(chalk.gray("Run 'cstl init' first."));
         emitEarly("blocked_not_initialized");
@@ -1839,14 +1877,31 @@ export async function update(options) {
     }
     // Execute migrations if --migrate flag is set
     if (options.migrate && classifiedMigrations) {
+        const pendingRenameItems = [
+            ...classifiedMigrations.auto,
+            ...classifiedMigrations.confirm,
+            ...classifiedMigrations.conflict,
+        ];
+        if (includesCstlRuntimeDirRename(pendingRenameItems)) {
+            const assessment = assessCstlDirectoryMigrate(cwd, {
+                forceCstlMigrate: options.forceCstlMigrate,
+            });
+            if (!assessment.ok) {
+                console.error(chalk.red("Error:"), assessment.reason);
+                process.exit(1);
+            }
+        }
         migrationApplyResult = await executeMigrations(classifiedMigrations, cwd, {
             force: options.force,
             skipAll: options.skipAll,
         });
         printMigrationResult(migrationApplyResult);
+        if (includesCstlRuntimeDirRename(pendingRenameItems)) {
+            upgradeAgentsMdToCstlMarkers(cwd);
+        }
         // Hardcoded: Rename traces-*.md to journal-*.md in workspace directories
         // Why hardcoded: The migration system only supports fixed path renames, not pattern-based.
-        // traces-*.md files are in .trellis/workspace/{developer}/ with variable developer names
+        // traces-*.md files are in .cstl/workspace/{developer}/ with variable developer names
         // and variable file numbers (traces-1.md, traces-2.md, etc.), so we can't enumerate them
         // in the migration manifest. This is a one-time migration for the 0.2.0 naming redesign.
         const workspaceDir = path.join(cwd, PATHS.WORKSPACE);