@skaile/workspaces 5.7.0 → 5.8.0

package/dist/cli/index.js

@@ -1,24 +1,24 @@
 #!/usr/bin/env node
-import { makeProvidersCommand, loadRegistryView, addProviderEntry, ProviderRegistryWriteError } from '../chunk-53MSCGR2.js';
-import { makeSourceCommand, syncProjectSources } from '../chunk-IZLQ4GDO.js';
-import { makeInstallCommand, makeCheckCommand, makeCleanCommand, REF_HINT, reportInstalledSoftDeps } from '../chunk-EU3Q5AQ4.js';
+import { makeProvidersCommand, loadRegistryView, addProviderEntry, ProviderRegistryWriteError } from '../chunk-NPLPCRW5.js';
+import { makeSourceCommand, syncProjectSources } from '../chunk-P23M65LB.js';
+import { makeInstallCommand, makeCheckCommand, makeCleanCommand, reportRelocked, REF_HINT, reportInstalledSoftDeps } from '../chunk-GXXFLBUQ.js';
 import { createSpinner } from '../chunk-NESV47MF.js';
-import { AI_RESOURCES } from '../chunk-7FJQT3GT.js';
-import { findAssetManifestFile, declaredVersion, checkAssetManifest } from '../chunk-6C654TFI.js';
-import { getStoreConfig, storeFetch, deviceLogin, loadStoreAuthConfig, logout, hasStoredAuth, isStoreAuthenticated, getStoreToken, getStoreIdentity, assetEntryRef, refFor } from '../chunk-LXY4BUA3.js';
-import { openCatalogSource, LocalCatalogDisabledError, openLibraryManager, openLibrary } from '../chunk-GIC3G5YG.js';
-import { logErr, S, logOk, logInfo, logWarn, TARGET_DEFAULT_HINT, deferredWarnings, warnLegacyClaudeCopies, kindColorPad, kindColor, colorRef, formatSoftDepSection, bareSoftDepName, formatSoftDepHint, formatRelativeTime, formatSoftDepRemovePreview, formatSoftDepAddPreview, fitWidth, KIND_COL_WIDTH } from '../chunk-THEJJBOU.js';
-import { getKindRegistry, getKnownKinds } from '../chunk-WIEC3ZE4.js';
+import { AI_RESOURCES } from '../chunk-Y4N2NUZD.js';
+import { findAssetManifestFile, declaredVersion, readAssetBody, checkAssetManifest } from '../chunk-ZAOGFXDO.js';
+import { getStoreConfig, storeFetch, deviceLogin, loadStoreAuthConfig, logout, hasStoredAuth, isStoreAuthenticated, getStoreToken, getStoreIdentity, assetEntryRef, manifestVersionMismatchMessage, refFor } from '../chunk-HYDRDNKN.js';
+import { openCatalogSource, LocalCatalogDisabledError, openLibraryManager, openLibrary } from '../chunk-HG34RNTK.js';
+import { logErr, S, logOk, logInfo, logWarn, TARGET_DEFAULT_HINT, deferredWarnings, warnLegacyClaudeCopies, kindColorPad, kindColor, colorRef, formatSoftDepSection, bareSoftDepName, formatSoftDepHint, formatRelativeTime, formatSoftDepRemovePreview, formatSoftDepAddPreview, fitWidth, KIND_COL_WIDTH } from '../chunk-F2EKONM7.js';
+import { getKindRegistry, getKnownKinds } from '../chunk-2FRUUDZY.js';
 import { LocalSecretsProvider } from '../chunk-ILFGVSTJ.js';
-import { runAgentChat, isCompositionError, loadSessionById, loadSession, listSessions, setCurrentSession, deleteSession, clearSession, loadAgentManifest, hashAgentFiles, createCompositionContentSource, compileComposition, instanceForSession, resolveAgentInstance, describeComposition, MarkdownStreamer } from '../chunk-VOOI7B2L.js';
-import { buildClaudePluginFiles } from '../chunk-N6FBTXQ5.js';
-import '../chunk-6UFFKMVC.js';
-import '../chunk-KM7XWC4Y.js';
+import { runAgentChat, isCompositionError, loadSessionById, loadSession, listSessions, setCurrentSession, deleteSession, clearSession, loadAgentManifest, hashAgentFiles, createCompositionContentSource, compileComposition, instanceForSession, resolveAgentInstance, describeComposition, MarkdownStreamer } from '../chunk-LEMHVDET.js';
+import { buildClaudePluginFiles } from '../chunk-I6NLLJHZ.js';
+import '../chunk-LSXHED6I.js';
+import '../chunk-UAROCOXF.js';
 import '../chunk-R6O6YWU7.js';
-import '../chunk-IUUYRXT6.js';
-import '../chunk-RNPHRRLG.js';
+import '../chunk-W5DWWE4Y.js';
+import '../chunk-4PTSR4UU.js';
 import '../chunk-4ZTPYIBE.js';
-import '../chunk-NWQB7UTY.js';
+import '../chunk-IONAUNWB.js';
 import '../chunk-X5YPJV4N.js';
 import '../chunk-O7SG5PC2.js';
 import '../chunk-7QBNJTTQ.js';
@@ -26,60 +26,59 @@ import '../chunk-OBYKJB4U.js';
 import '../chunk-5LKOAX7I.js';
 import '../chunk-32NA4TVC.js';
 import '../chunk-W3UDISS2.js';
-import '../chunk-HCYS7GFP.js';
-import { runFlow, resumeFlow } from '../chunk-MKLBK7HI.js';
+import '../chunk-V2DXZYBB.js';
+import { runFlow, resumeFlow } from '../chunk-ZKSJMZKD.js';
 import '../chunk-4R6DROGN.js';
-import { validateFlowVersions, parseSkillFrontmatter } from '../chunk-EB4XN3KE.js';
-import '../chunk-O4Z7MAW7.js';
-import '../chunk-CT6NQSA4.js';
-import '../chunk-SZWRPEF7.js';
-import '../chunk-FK6HPLQA.js';
-import '../chunk-PSA6ONFB.js';
-import '../chunk-34C42MJX.js';
-import '../chunk-UX3K4RKE.js';
-import '../chunk-EINLFFP6.js';
+import { validateFlowVersions, parseSkillFrontmatter } from '../chunk-CGT45WN7.js';
+import '../chunk-2LWYNQK7.js';
+import '../chunk-ISHJITXJ.js';
+import '../chunk-FTJJO3EM.js';
+import '../chunk-WTQ3TATB.js';
+import '../chunk-FVJK4QWM.js';
+import '../chunk-6GRX5L6A.js';
+import '../chunk-S53LOR7B.js';
 import '../chunk-LOO5CB5M.js';
-import '../chunk-NARITJS2.js';
-import '../chunk-GWXFSLBK.js';
-import '../chunk-XBSQ4KMC.js';
+import '../chunk-GCICGXDD.js';
+import '../chunk-PTSGWKHR.js';
+import '../chunk-B4X2N7JQ.js';
 import '../chunk-YROR332M.js';
-import { getProviderPreset, AI_PROVIDER_PRESETS } from '../chunk-BTK7ECLH.js';
+import { getProviderPreset, AI_PROVIDER_PRESETS } from '../chunk-AWQYXZVG.js';
 import '../chunk-6E6PKKAD.js';
 import '../chunk-IFGTRL2I.js';
-import { projectAiAssetsRoots, loadFlow, loadAllFlowEntries, findFlowFileInRoots } from '../chunk-LBQ4BBX4.js';
-import '../chunk-37FTLYFP.js';
-import '../chunk-QZLWJETK.js';
-import '../chunk-XUUYAS3Z.js';
-import { nodeLabel, nodeSkillAsset, nodeIsInert, nodeIsOptional, nodeRunKind, flowSkillVersionPins } from '../chunk-NFGRW3L7.js';
-import '../chunk-QCI6D7E4.js';
-import '../chunk-DMLDYFDS.js';
-import { AssetManager, MissingManifestError, parseRefTolerant, normalizeRepoUrl, FACTORY_SOURCE_URL } from '../chunk-D5HOETOB.js';
-import { cloneOrInitGitRepo, trackOriginBranch, ensureGitRepo, setManifestPublisher, LIBRARY_OWNERSHIPS, syncManifestWithDisk, isGitRepo, assertManifestEditable, installLibraryAsset, missingRootAssets, assertValidLibraryName, stampManifestPublisher, upsertManifestAsset, getStoreManifestsDir, getDefaultValue, isSecretPlaceholder } from '../chunk-DFFD4BFG.js';
-import { parseManifestFile, requiresSyntaxErrors, SEMVER_RE } from '../chunk-6VRJH4MR.js';
-import '../chunk-FAP63KV7.js';
+import { projectAiAssetsRoots, loadFlow, loadAllFlowEntries, findFlowFileInRoots } from '../chunk-FZNG4V4J.js';
+import '../chunk-LNFKL23K.js';
+import '../chunk-MGGFBZWA.js';
+import '../chunk-M3WPBTGJ.js';
+import { nodeLabel, nodeSkillAsset, nodeIsInert, nodeIsOptional, nodeRunKind, flowSkillVersionPins } from '../chunk-7RGTAEG6.js';
+import '../chunk-NUELZWCF.js';
+import '../chunk-F3RDEH5U.js';
+import { AssetManager, MissingManifestError, parseRefTolerant, normalizeRepoUrl, FACTORY_SOURCE_URL } from '../chunk-H7QUDDKH.js';
+import { cloneOrInitGitRepo, trackOriginBranch, stampManifestPublisher, ensureGitRepo, conflictingAssetRoot, setManifestPublisher, LIBRARY_OWNERSHIPS, isGitRepo, assertManifestEditable, installLibraryAsset, missingRootAssets, assertValidLibraryName, upsertManifestAsset, syncManifestWithDisk, getStoreManifestsDir, getDefaultValue, isSecretPlaceholder } from '../chunk-4MQS7CAF.js';
+import { parseManifestFile, requiresSyntaxErrors, SEMVER_RE } from '../chunk-Y7QA2OLD.js';
+import '../chunk-CKQEIY43.js';
 import '../chunk-R7FOF242.js';
 import '../chunk-3TXEJN4W.js';
-import { installTargetOf, SCAFFOLD_KINDS } from '../chunk-74EEFB52.js';
+import { installTargetOf, SCAFFOLD_KINDS } from '../chunk-YSHVQGUS.js';
 import '../chunk-CGYEHQOX.js';
 import '../chunk-KTBKW2FI.js';
 import '../chunk-UQ6LFBPZ.js';
-import '../chunk-AVCUPPG6.js';
-import { effectiveComposes, validatePreset, composeSlotDiagnostics, agentDeprecationDiagnostics, validateAgent, SLOT_ID_PATTERN } from '../chunk-FRHE7FFB.js';
-import { resolveSettings, globalSettingsPath, projectSettingsPath, loadSettings, saveSettings, WorkspaceYamlEditor, resolveLibraryDir, checkAgentSkillConformance, globalInstallDir, GLOBAL_INSTALL_DIR_NAME, readLock, aiResourceRoots, workspaceProviderRegistryPath, userProviderRegistryPath, loadProviderRegistryFile } from '../chunk-OOLT6HGP.js';
+import '../chunk-EF7NPDDU.js';
+import { effectiveComposes, validatePreset, composeSlotDiagnostics, agentDeprecationDiagnostics, validateAgent, SLOT_ID_PATTERN } from '../chunk-B6GIW55K.js';
+import { resolveSettings, globalSettingsPath, projectSettingsPath, loadSettings, saveSettings, WorkspaceYamlEditor, resolveLibraryDir, checkAgentSkillConformance, globalInstallDir, GLOBAL_INSTALL_DIR_NAME, readLock, aiResourceRoots, workspaceProviderRegistryPath, userProviderRegistryPath, loadProviderRegistryFile } from '../chunk-36AFURKZ.js';
 import '../chunk-4GY63JU6.js';
-import { factoryAssetRoots } from '../chunk-SWO25LTO.js';
-import '../chunk-G67BOI2J.js';
+import { factoryAssetRoots } from '../chunk-GB7WDMH2.js';
+import '../chunk-PMECEZK3.js';
 import { DEFAULT_DRIVER_ID, DRIVER_DEFAULTS } from '../chunk-5BEFNLOR.js';
 import { findKindDirs } from '../chunk-A2ULN3KX.js';
-import { sourceCacheKey, getGlobalCacheDir, resolveAgentDir, AgentRefResolutionError, resolveAgentDefinitionDir, resolveSkWorkspaceConfig, matchPin, coerceVersion, loadSkWorkspaceConfig, normalizeAgentInstances, agentInstanceDiagnostics, storeManifestSlug, isWorkspaceConfigFilename } from '../chunk-LCU5U5IW.js';
+import { sourceCacheKey, getGlobalCacheDir, resolveAgentDir, AgentRefResolutionError, resolveAgentDefinitionDir, resolveSkWorkspaceConfig, matchPin, coerceVersion, loadSkWorkspaceConfig, normalizeAgentInstances, agentInstanceDiagnostics, storeManifestSlug, isWorkspaceConfigFilename } from '../chunk-JAKOMFC6.js';
 import { globalCacheRoot, globalSkaileDir, userConfigPath } from '../chunk-L5VSIPQD.js';
 import { SUPPORTED_DRIVER_TARGETS, driverTargetForDriver } from '../chunk-CPSIPIX7.js';
-import { SKAILE_MANIFEST_FILENAME, loadSkPublishManifest, decodeSkaileManifest, encodeSkaileManifest } from '../chunk-RVIZQ5XD.js';
+import { SKAILE_MANIFEST_FILENAME, decodeSkaileManifest, loadSkPublishManifest, encodeSkaileManifest } from '../chunk-BTE2V4IW.js';
 import { pluginTitle } from '../chunk-RVRB27AN.js';
-import { parseFrontmatter, scanDirectory } from '../chunk-TTPSDC2G.js';
-import { parseAssetRef, isValidPublisher, PUBLISHER_HINT, isValidAssetName, ASSET_NAME_HINT, slugifyAssetName, parseAssetRefLoose, assetRefToStr } from '../chunk-O7VPNKYN.js';
+import { parseFrontmatter, scanDirectory } from '../chunk-GTILM2CI.js';
+import { parseAssetRef, isValidPublisher, PUBLISHER_HINT, isValidAssetName, ASSET_NAME_HINT, slugifyAssetName, parseAssetRefLoose, assetRefToStr } from '../chunk-QVNRCDTV.js';
 import { portableSpawn, portableSpawnSync } from '../chunk-ICSCSM5D.js';
-import { openSqlite } from '../chunk-JMKB7IB4.js';
+import { openSqlite } from '../chunk-UMVKJM4Q.js';
 import { parseModelRef, resolveEntryBaseUrl } from '../chunk-MJHSLODD.js';
 import '../chunk-C3CAXQMA.js';
 import '../chunk-BOFL7GIF.js';
@@ -185,7 +184,7 @@ async function runSearch(kind, query, opts) {
   }
 }
 async function searchIndex(query, kind) {
-  const { openLibrary: openLibrary2 } = await import('../open-library-P3D337NH.js');
+  const { openLibrary: openLibrary2 } = await import('../open-library-OG457THY.js');
   const library = await openLibrary2();
   try {
     const defs = await library.listAssetDefs(kind ? { kind } : {});
@@ -238,12 +237,44 @@ function unionEntries(indexed, factory) {
   const seen = new Set(indexed.map(entryDedupKey));
   return [...indexed, ...factory.filter((e) => !seen.has(entryDedupKey(e)))];
 }
+async function expandLibraryCopies(entries, projectDir) {
+  if (entries.length === 0) return entries;
+  let holders;
+  try {
+    holders = await new AssetManager({ registry: getKindRegistry(), projectDir }).libraryHolders();
+  } catch {
+    return entries;
+  }
+  if (holders.size === 0) return entries;
+  const out = [];
+  const expanded = /* @__PURE__ */ new Set();
+  for (const e of entries) {
+    const key = e.publisher ? `${e.kind}:@${e.publisher}/${e.name}` : void 0;
+    const group = key ? holders.get(key) : void 0;
+    if (!key || !group) {
+      out.push(e);
+      continue;
+    }
+    if (expanded.has(key)) continue;
+    expanded.add(key);
+    for (const h of group) {
+      out.push({
+        ...e,
+        version: h.version,
+        description: h.description || e.description,
+        library: h.library,
+        usedByAdd: h.picked
+      });
+    }
+  }
+  return out;
+}
 async function searchLocal(query, kind, opts, showStore, airGapped) {
   const projectDir = path23__default.resolve(opts.projectDir);
   const factory = await searchFactory(projectDir, query, kind);
   let entries = unionEntries(await searchIndex(query, kind), factory);
   if (entries.length === 0 && !query && !kind && !airGapped) {
-    const { autoSyncForSearch } = await import('../source-FYVSFYEI.js');
+    const { autoSyncForSearch } = await import('../source-LKOFTOEK.js');
     if (await autoSyncForSearch(projectDir)) {
       entries = unionEntries(await searchIndex(query, kind), factory);
     }
@@ -260,7 +291,7 @@ async function searchLocal(query, kind, opts, showStore, airGapped) {
     console.log(`
   ${S.heading("Local:")}`);
   }
-  printLocalEntries(entries);
+  printLocalEntries(await expandLibraryCopies(entries, projectDir));
 }
 var MIN_LOCAL_DESCRIPTION_WIDTH = 10;
 function layoutLocalTable(rows, width, style = {}) {
@@ -324,7 +355,7 @@ function printLocalEntries(entries, width = terminalWidth()) {
         ref: localEntryRef(e),
         description: e.description,
         version: e.version ? `v${e.version}` : "",
-        library: e.library
+        library: e.usedByAdd ? `${e.library} (used by add)` : e.library
       })),
       width,
       { ref: S.cmd, version: S.dim, library: S.dim }
@@ -361,7 +392,7 @@ async function searchStore(query, kind, opts, airGapped) {
     logInfo("air-gapped (cache_ttl: 0) \u2014 local sources only");
     return;
   }
-  const { openCatalogSource: openCatalogSource2, LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-P3D337NH.js');
+  const { openCatalogSource: openCatalogSource2, LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-OG457THY.js');
   try {
     const remote = await openCatalogSource2({ projectDir: path23__default.resolve(opts.projectDir) });
     const assets = await remote.listAssets(kind ? { kind } : {});
@@ -435,6 +466,12 @@ async function promptSoftDepAdds(am2, ref, io) {
     if (yes === true) await addEdge(edge.toRef);
   }
 }
+function presetAddNote(ref, presets) {
+  const own = presets.find((p6) => p6.ref.split("#")[0] === ref.split("#")[0]);
+  if (!own) return void 0;
+  const origin = own.library ? `library ${own.library}` : "a source or store";
+  return `Recorded in skaile.yaml (preset from ${origin}). ${own.assets} assets, ${own.skipped} instance items skipped (apply with skaile preset apply).`;
+}
 async function reportPresetMembership(am2, ref, onHint) {
   for (const preset of await am2.presetsContaining(ref)) {
     onHint(
@@ -491,9 +528,13 @@ function makeAddCommand() {
     spinner.start(`Adding ${ref}`);
     try {
       const libraryOf = /* @__PURE__ */ new Map();
+      let presets = [];
       const added = await am2.add(ref, {
         link: opts.link,
-        onLibraryOrigin: (deployedRef, library) => libraryOf.set(deployedRef, library)
+        onLibraryOrigin: (deployedRef, library) => libraryOf.set(deployedRef, library),
+        onPresets: (expanded) => {
+          presets = expanded;
+        }
       });
       spinner.stop("Done");
       warnings.flush();
@@ -510,7 +551,9 @@ function makeAddCommand() {
       });
       if (added.length === 0) {
         const kind = parseAssetRef(ref).kind;
-        if (!installTargetOf(getKindRegistry(), kind))
+        const presetNote = presetAddNote(ref, presets);
+        if (presetNote) logInfo(presetNote);
+        else if (!installTargetOf(getKindRegistry(), kind))
           logInfo(
             `Recorded in skaile.yaml (store bytes are fetched + verified into .skaile/cache/store). ${kind} assets are not deployed into the driver target \u2014 they are composed when skaile runs the agent.`
           );
@@ -531,7 +574,7 @@ function makeAddCommand() {
   });
 }
 function makeRemoveCommand() {
-  return new Command("remove").description("Remove from skaile.yaml + undeploy").argument("<ref>", "Asset reference (kind:name)").option("--project-dir <path>", "Project directory", process.cwd()).option("--global", "Remove from ~/.skaile/skaile.yaml + undeploy from every global harness").option(
+  return new Command("remove").description("Remove from skaile.yaml + undeploy").argument("<ref>", "Asset reference (kind:@publisher/name, or kind:name)").option("--project-dir <path>", "Project directory", process.cwd()).option("--global", "Remove from ~/.skaile/skaile.yaml + undeploy from every global harness").option(
     "--harness <ids>",
     "Comma-separated global harnesses to undeploy from (default: all resolved); implies --global"
   ).option("--target <agent>", `Driver target (${TARGET_DEFAULT_HINT})`).option("--no-soft-deps", "skip the orphaned-soft-dep prompt (don't remove, don't report)").action(async (ref, opts) => {
@@ -543,13 +586,23 @@ function makeRemoveCommand() {
       harnesses,
       driverTarget: opts.target
     });
-    const ok = am2.remove(ref);
-    if (!ok) {
+    let result;
+    try {
+      result = await am2.removeWithDependencies(ref);
+    } catch (err2) {
+      logErr(err2 instanceof Error ? err2.message : String(err2));
+      process.exitCode = 1;
+      return;
+    }
+    if (!result.changed) {
       logErr(`Not deployed or declared: ${ref}`);
       process.exitCode = 1;
       return;
     }
     logOk(`Removed ${ref}`);
+    for (const dep of result.pruned) {
+      logOk(`Removed ${dep} (no longer required by anything declared in skaile.yaml)`);
+    }
     await promptSoftDepRemovals(am2, ref, {
       isTTY: !!process.stdin.isTTY,
       noSoftDeps: opts.softDeps === false,
@@ -703,7 +756,7 @@ async function resolveInfoEntry(am2, ref, opts) {
     return { entry: match ?? deployed };
   }
   const lookup = opts.storeLookup ?? (async (filter) => {
-    const { resolveCatalogSource } = await import('../open-library-P3D337NH.js');
+    const { resolveCatalogSource } = await import('../open-library-OG457THY.js');
     const { source, close } = await resolveCatalogSource({ projectDir: opts.projectDir });
     try {
       return await source.listAssets(filter);
@@ -719,7 +772,7 @@ async function resolveInfoEntry(am2, ref, opts) {
     );
     return { entry: hit ? catalogAssetToEntry(hit) : null };
   } catch (err2) {
-    const { LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-P3D337NH.js');
+    const { LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-OG457THY.js');
     const storeNote = err2 instanceof Error ? err2.message : String(err2);
     const disabled = err2 instanceof LocalCatalogDisabledError2 || /catalog\.url/i.test(storeNote);
     return { entry: null, storeNote, ...disabled ? { storeDisabled: true } : {} };
@@ -754,8 +807,10 @@ function makeInfoCommand() {
     console.log(`  source:      ${S.dim(entry.source)}`);
     if (entry.requires.length) {
       console.log(`  requires:`);
-      for (const d of entry.requires)
-        console.log(`    ${S.dim("\xB7")}  ${kindColor(d.kind)}:${d.name}`);
+      for (const d of entry.requires) {
+        const scope = d.publisher ? `@${d.publisher}/` : "";
+        console.log(`    ${S.dim("\xB7")}  ${kindColor(d.kind)}:${scope}${d.name}`);
+      }
     }
     if (entry.dependencies.length) {
       console.log(`  dependencies:`);
@@ -795,7 +850,7 @@ function makeDoctorCommand() {
     const missing = issues.filter((i) => !i.unresolved);
     for (const i of unresolved) {
       logErr(
-        `${i.assetKind}:${i.assetName}: locked, but no source or library provides it \u2014 run skaile install`
+        `${i.assetKind}:${i.assetName}: locked, but no source or library provides it \u2014 ${i.fix ?? "run skaile install"}`
       );
     }
     if (missing.length === 0) return;
@@ -923,8 +978,8 @@ function rejectRemovedDomainOption(opts) {
   logErr(DOMAIN_REMOVED_HINT);
   process.exit(1);
 }
-function countDomainFiles(root) {
-  let count = 0;
+function findFiles(root, match) {
+  const found = [];
   const walk = (dir) => {
     let entries;
     try {
@@ -937,13 +992,16 @@ function countDomainFiles(root) {
         if (!entry.name.startsWith(".") && entry.name !== "node_modules") {
           walk(path23.join(dir, entry.name));
         }
-      } else if (entry.name === "DOMAIN.md") {
-        count++;
+      } else if (match(entry.name)) {
+        found.push(path23.join(dir, entry.name));
       }
     }
   };
   walk(root);
-  return count;
+  return found;
+}
+function countDomainFiles(root) {
+  return findFiles(root, (name) => name === "DOMAIN.md").length;
 }
 function warnIgnoredDomainFiles(root) {
   const count = countDomainFiles(root);
@@ -954,6 +1012,17 @@ function warnIgnoredDomainFiles(root) {
   }
   return count;
 }
+function warnLegacyBundleFiles(root) {
+  const files = findFiles(root, (name) => name.endsWith(".bundle.yaml"));
+  if (files.length > 0) {
+    const shown = files.slice(0, 5).map((f) => path23.relative(root, f) || f);
+    const more = files.length > shown.length ? `, +${files.length - shown.length} more` : "";
+    logWarn(
+      `${files.length} *.bundle.yaml file(s) are not scanned (the bundle kind became preset): ${shown.join(", ")}${more}. Run \`skaile migrate assets ${root} --write\` to rename them to *.preset.yaml. See ${LIBRARY_UPGRADE_DOCS}`
+    );
+  }
+  return files.length;
+}
 var DEFAULT_IMPORT_VERSION = "0.1.0";
 var DEFAULT_IMPORT_STAGE = "alpha";
 function claudeSkillRoots() {
@@ -1070,6 +1139,13 @@ function makeAssetCommand() {
   ).option("--commit", "Auto-commit in git-backed libraries", false).action(
     async (nameOrPath, opts) => {
       rejectRemovedDomainOption(opts);
+      if (opts.publisher !== void 0) {
+        const bare = opts.publisher.trim().replace(/^@/, "");
+        if (!isValidPublisher(bare)) {
+          logErr(`Invalid publisher "${opts.publisher}": ${PUBLISHER_HINT}.`);
+          process.exit(1);
+        }
+      }
       const src = resolveImportSource(nameOrPath);
       if (!src) {
         logErr(
@@ -1115,6 +1191,13 @@ function makeAssetCommand() {
           logErr(`Destination already exists: ${destDir}`);
           process.exit(1);
         }
+        const taken = conflictingAssetRoot(target.path, "skill", norm.name, norm.name);
+        if (taken) {
+          logErr(
+            `skill:${norm.name} already exists at "${taken}" \u2014 importing it again would re-point the manifest entry. Rename the skill first.`
+          );
+          process.exit(1);
+        }
         fs9.cpSync(src.dir, destDir, { recursive: true });
         fs9.writeFileSync(path23.join(destDir, "SKILL.md"), norm.content, "utf8");
         for (const note of norm.notes) logInfo(`  \u2022 ${note}`);
@@ -1182,10 +1265,10 @@ function makeAssetCommand() {
           );
           process.exit(1);
         }
-        const basename2 = path23.basename(srcPath);
+        const basename3 = path23.basename(srcPath);
         const destDir = target.path;
         fs9.mkdirSync(destDir, { recursive: true });
-        const destPath = path23.join(destDir, basename2);
+        const destPath = path23.join(destDir, basename3);
         if (fs9.existsSync(destPath)) {
           logErr(`Destination already exists: ${destPath}`);
           process.exit(1);
@@ -1204,7 +1287,7 @@ function makeAssetCommand() {
         if (target.backend === "git" && opts.commit) {
           const { spawnSync: spawnSync2 } = await import('child_process');
           spawnSync2("git", ["add", "--", destPath], { cwd: target.path, stdio: "inherit" });
-          const r = spawnSync2("git", ["commit", "-m", `skaile: migrate ${basename2}`], {
+          const r = spawnSync2("git", ["commit", "-m", `skaile: migrate ${basename3}`], {
             cwd: target.path,
             stdio: "inherit"
           });
@@ -1212,7 +1295,7 @@ function makeAssetCommand() {
             logWarn("Nothing committed (working tree clean or commit aborted).");
           }
         }
-        logOk(`Migrated ${basename2} \u2192 ${target.name} (${opts.mode})`);
+        logOk(`Migrated ${basename3} \u2192 ${target.name} (${opts.mode})`);
         if (opts.mode === "move") {
           logInfo("Source moved into the library \u2014 future edits modify the library copy.");
         } else if (opts.mode === "copy") {
@@ -1453,7 +1536,7 @@ function makeCatalogCommand() {
   return catalog;
 }
 async function runLocalCatalogTest(projectDir) {
-  const { resolveCatalogSource } = await import('../open-library-P3D337NH.js');
+  const { resolveCatalogSource } = await import('../open-library-OG457THY.js');
   let resolved;
   try {
     resolved = await resolveCatalogSource({ projectDir });
@@ -1593,29 +1676,20 @@ function libraryFlowEntries() {
 async function scanLibraryFlowEntries() {
   const entries = [];
   try {
-    const { LocalCatalogSource, LocalIndex, resolveIndexPath } = await import('../library/index.js');
+    const { LocalIndex, resolveIndexPath, scanAuthoringLibraries } = await import('../library/index.js');
     const indexPath = resolveIndexPath();
     if (!existsSync(indexPath)) return entries;
-    const [{ authoringLibraries }, { getKindRegistry: getKindRegistry2 }] = await Promise.all([
-      import('../open-library-P3D337NH.js'),
-      import('../open-registry-Z3P2X2AB.js')
-    ]);
+    const { getKindRegistry: getKindRegistry2 } = await import('../open-registry-ZUZJ7MS7.js');
     const index = new LocalIndex({ indexPath });
     try {
-      const registry = getKindRegistry2();
-      for (const lib of authoringLibraries(await index.listSources())) {
-        if (!existsSync(lib.path)) continue;
-        try {
-          const { assets } = new LocalCatalogSource(index, lib.id, lib.path, registry).scan();
-          for (const asset of assets) {
-            if (asset.kind !== "flow") continue;
-            try {
-              const flow = loadFlow(asset.manifestPath);
-              if (flow.id) entries.push({ flow, path: asset.manifestPath });
-            } catch {
-            }
+      for (const { assets } of await scanAuthoringLibraries(index, getKindRegistry2())) {
+        for (const asset of assets) {
+          if (asset.kind !== "flow") continue;
+          try {
+            const flow = loadFlow(asset.manifestPath);
+            if (flow.id) entries.push({ flow, path: asset.manifestPath });
+          } catch {
           }
-        } catch {
         }
       }
     } finally {
@@ -2558,7 +2632,7 @@ async function ensureTargetsRegistered(projectDir) {
   const { resolveSkWorkspaceConfig: resolveSkWorkspaceConfig2 } = await import('../core/index.js');
   const config = resolveSkWorkspaceConfig2(projectDir);
   if (config.plugins && config.plugins.length > 0) {
-    const { ensurePluginsLoaded } = await import('../plugin-store-WI4MZJLP.js');
+    const { ensurePluginsLoaded } = await import('../plugin-store-MPAMD5OT.js');
     const result = await ensurePluginsLoaded(projectDir, config.plugins, pluginRegistry);
     for (const f of result.failed) logWarn(f.error);
   }
@@ -3394,7 +3468,6 @@ function exitOnSyncError(err2) {
 }
 var UNFINISHED_GIT_ENTRIES = {
   MERGE_HEAD: "a merge in progress",
-  REBASE_HEAD: "a rebase in progress",
   "rebase-merge": "a rebase in progress",
   "rebase-apply": "a rebase in progress",
   CHERRY_PICK_HEAD: "a cherry-pick in progress",
@@ -3411,6 +3484,80 @@ function unfinishedGitState(dir) {
   }
   return null;
 }
+async function reindexLibrary(lib, library, name) {
+  assertManifestEditableOrExit(lib.path);
+  const badRequires = manifestRequiresProblems(lib.path);
+  const resolved = resolveLibraryPublisherDetailed(lib, {}, getStoreIdentity());
+  warnLibraryNameFallback(name, resolved);
+  const { removed, unknownKind, skipped } = await syncManifestWithDisk(
+    lib.path,
+    resolved.publisher,
+    getKindRegistry()
+  );
+  const manifest = loadSkPublishManifest(lib.path);
+  for (const a of unknownKind) {
+    logWarn(
+      `Removed manifest entry ${a.kind}:${a.name}: the kind "${a.kind}" is not registered (removed or renamed in a newer release).`
+    );
+  }
+  for (const a of removed) {
+    const ref = manifest ? assetEntryRef(a, manifest) : `${a.kind}:${a.name}`;
+    logInfo(`Removed manifest entry ${ref} (root ${a.root} is gone)`);
+  }
+  for (const s of skipped.filter((x) => x.reason === "invalid-version")) {
+    logWarn(
+      `${s.kind}:${s.name} skipped: ${s.detail}. Set a valid \`metadata.version\` (e.g. 0.1.0) and re-run \`skaile library index ${name}\`.`
+    );
+  }
+  const duplicates = skipped.filter((x) => x.reason === "duplicate");
+  for (const s of duplicates) {
+    logErr(
+      `${s.kind}:${s.name} found in ${path23.dirname(s.file)} but ${s.detail}. Rename or delete one of the two directories, then re-run \`skaile library index ${name}\`.`
+    );
+  }
+  const duplicateFiles = new Set(duplicates.map((s) => path23.resolve(lib.path, s.file)));
+  const skippedKeys = new Set(
+    skipped.filter((s) => s.reason !== "duplicate").map((s) => `${s.kind}:${s.name}`)
+  );
+  const res = await indexLibrary(lib, library, {
+    exclude: (a) => skippedKeys.has(`${a.kind}:${a.name}`) || duplicateFiles.has(path23.resolve(a.manifestPath))
+  });
+  const unparsable = res.errors.filter((e) => e.includes("ManifestSchemaError:"));
+  for (const e of res.errors) (unparsable.includes(e) ? logErr : logWarn)(e);
+  const syncUnparsable = skipped.filter(
+    (s) => s.reason === "unparsable" && !unparsable.some((e) => e.includes(s.file))
+  );
+  for (const s of syncUnparsable) {
+    logErr(`${s.kind}:${s.name} skipped: manifest file ${s.file} could not be parsed.`);
+  }
+  for (const p6 of badRequires) logErr(`${p6.asset}: ${p6.message}`);
+  logOk(`Indexed ${res.assetsUpdated} asset(s) from ${name}.`);
+  warnIgnoredDomainFiles(lib.path);
+  warnLegacyBundleFiles(lib.path);
+  const skippedUnparsable = unparsable.length + syncUnparsable.length;
+  if (skippedUnparsable > 0) {
+    logErr(`${skippedUnparsable} asset(s) skipped: manifest could not be parsed.`);
+    process.exitCode = 1;
+  }
+  if (badRequires.length > 0) {
+    logErr(
+      `${badRequires.length} invalid requires entr${badRequires.length === 1 ? "y" : "ies"} ignored: use the \`kind:@<publisher>/name[#version]\` form.`
+    );
+    process.exitCode = 1;
+  }
+  if (duplicates.length > 0) {
+    logErr(
+      `${duplicates.length} asset(s) skipped: kind + name already registered in another directory.`
+    );
+    process.exitCode = 1;
+  }
+}
+async function indexPulledLibrary(lib, library, name) {
+  const res = await indexLibrary(lib, library);
+  for (const e of res.errors) logWarn(e);
+  logOk(`Indexed ${res.assetsUpdated} asset(s) from ${name}.`);
+  warnIgnoredDomainFiles(lib.path);
+}
 function assertManifestEditableOrExit(libraryPath) {
   try {
     assertManifestEditable(libraryPath);
@@ -3426,13 +3573,21 @@ async function assertLibraryPathFree(manager, dir, exceptId) {
 }
 function canonicalDir(dir) {
   const abs = path23.resolve(dir);
-  return fs9.existsSync(abs) ? fs9.realpathSync(abs) : abs;
+  const missing = [];
+  let existing = abs;
+  while (!fs9.existsSync(existing)) {
+    const parent = path23.dirname(existing);
+    if (parent === existing) return abs;
+    missing.unshift(path23.basename(existing));
+    existing = parent;
+  }
+  return path23.join(fs9.realpathSync(existing), ...missing);
 }
 function refuseGlobalInstallFolder(name, dir) {
   const reserved = globalInstallDir();
-  const rel = path23.relative(canonicalDir(reserved), canonicalDir(dir));
+  const rel = path23.relative(canonicalDir(reserved).toLowerCase(), canonicalDir(dir).toLowerCase());
   const inside = rel === "" || !rel.startsWith("..") && !path23.isAbsolute(rel);
-  if (name === GLOBAL_INSTALL_DIR_NAME || inside) {
+  if (name?.toLowerCase() === GLOBAL_INSTALL_DIR_NAME || inside) {
     logErr(
       `"${GLOBAL_INSTALL_DIR_NAME}" is reserved: ${reserved} holds assets from \`skaile install\`, not a library you author.`
     );
@@ -3478,7 +3633,7 @@ function pruneEmptyLibraryParents(libPath) {
   }
 }
 async function warnIfNotGithubRemote(name, url) {
-  const { isGithubRemote, notGithubRemoteMessage } = await import('../library-publish-FGXF5TJO.js');
+  const { isGithubRemote, notGithubRemoteMessage } = await import('../library-publish-PICMDSB2.js');
   if (!isGithubRemote(url)) logWarn(notGithubRemoteMessage(name, url));
 }
 function scaffoldLibraryFiles(dir, name) {
@@ -3656,6 +3811,9 @@ function makeLibraryCommand() {
             );
           }
           warnLibraryNameFallback(name, resolved);
+          if (resolved.source !== "manifest") {
+            stampManifestPublisher(lib.path, resolved.publisher);
+          }
           const res = await indexLibrary(lib, library);
           for (const e of res.errors) logWarn(e);
           logOk(`Indexed ${res.assetsUpdated} asset(s) from ${name}.`);
@@ -3735,6 +3893,18 @@ function makeLibraryCommand() {
           logErr(`--dir "${opts.dir}" must stay inside the library (${libRoot}).`);
           process.exit(1);
         }
+        const taken = conflictingAssetRoot(
+          libRoot,
+          effectiveKind,
+          name,
+          path23.relative(libRoot, path23.join(destDir, name))
+        );
+        if (taken) {
+          logErr(
+            `${effectiveKind}:${name} already exists at "${taken}" \u2014 creating it again under "${path23.relative(libRoot, destDir) || "."}" would re-point the manifest entry. Pick another name.`
+          );
+          process.exit(1);
+        }
         const res = am2.create(name, effectiveKind, destDir, { description: opts.description });
         if (!res.ok) {
           logErr(res.path);
@@ -3933,7 +4103,7 @@ function makeLibraryCommand() {
     }
   });
   cmd.command("sync <name>").description("Pull then push (as backend permits)").action(async (name) => {
-    const { manager, close } = await openLibraryManager();
+    const { manager, library, close } = await openLibraryManager();
     try {
       const lib = await manager.requireLibrary(name);
       requireGitBackend(lib, "sync");
@@ -3946,6 +4116,7 @@ function makeLibraryCommand() {
         logInfo(`Pushed: ${push.pushed}`);
       }
       await manager.updateLibrary(name, { lastSyncAt: /* @__PURE__ */ new Date() });
+      if (pull.applied > 0) await indexPulledLibrary(lib, library, name);
       logOk(`Synced ${name}.`);
     } catch (err2) {
       exitOnSyncError(err2);
@@ -3957,57 +4128,13 @@ function makeLibraryCommand() {
     const { manager, library, close } = await openLibraryManager();
     try {
       const lib = await manager.requireLibrary(name);
-      assertManifestEditableOrExit(lib.path);
-      const badRequires = manifestRequiresProblems(lib.path);
-      const resolved = resolveLibraryPublisherDetailed(lib, {}, getStoreIdentity());
-      warnLibraryNameFallback(name, resolved);
-      const { removed, skipped } = await syncManifestWithDisk(
-        lib.path,
-        resolved.publisher,
-        getKindRegistry()
-      );
-      const manifest = loadSkPublishManifest(lib.path);
-      for (const a of removed) {
-        const ref = manifest ? assetEntryRef(a, manifest) : `${a.kind}:${a.name}`;
-        logInfo(`Removed manifest entry ${ref} (root ${a.root} is gone)`);
-      }
-      for (const s of skipped.filter((x) => x.reason === "invalid-version")) {
-        logWarn(
-          `${s.kind}:${s.name} skipped: ${s.detail}. Set a valid \`metadata.version\` (e.g. 0.1.0) and re-run \`skaile library index ${name}\`.`
-        );
-      }
-      const skippedKeys = new Set(skipped.map((s) => `${s.kind}:${s.name}`));
-      const res = await indexLibrary(lib, library, {
-        exclude: (a) => skippedKeys.has(`${a.kind}:${a.name}`)
-      });
-      const unparsable = res.errors.filter((e) => e.includes("ManifestSchemaError:"));
-      for (const e of res.errors) (unparsable.includes(e) ? logErr : logWarn)(e);
-      const syncUnparsable = skipped.filter(
-        (s) => s.reason === "unparsable" && !unparsable.some((e) => e.includes(s.file))
-      );
-      for (const s of syncUnparsable) {
-        logErr(`${s.kind}:${s.name} skipped: manifest file ${s.file} could not be parsed.`);
-      }
-      for (const p6 of badRequires) logErr(`${p6.asset}: ${p6.message}`);
-      logOk(`Indexed ${res.assetsUpdated} asset(s) from ${name}.`);
-      warnIgnoredDomainFiles(lib.path);
-      const skippedUnparsable = unparsable.length + syncUnparsable.length;
-      if (skippedUnparsable > 0) {
-        logErr(`${skippedUnparsable} asset(s) skipped: manifest could not be parsed.`);
-        process.exitCode = 1;
-      }
-      if (badRequires.length > 0) {
-        logErr(
-          `${badRequires.length} invalid requires entr${badRequires.length === 1 ? "y" : "ies"} ignored: use the \`kind:@<publisher>/name[#version]\` form.`
-        );
-        process.exitCode = 1;
-      }
+      await reindexLibrary(lib, library, name);
     } finally {
       close();
     }
   });
   cmd.command("pull <name>").description("Pull from remote").action(async (name) => {
-    const { manager, close } = await openLibraryManager();
+    const { manager, library, close } = await openLibraryManager();
     try {
       const lib = await manager.requireLibrary(name);
       requireGitBackend(lib, "pull");
@@ -4016,6 +4143,7 @@ function makeLibraryCommand() {
         exitOnSyncError(new Error(res.conflicts[0].reason));
       } else {
         logOk(`Pulled ${res.applied} change(s).`);
+        if (res.applied > 0) await indexPulledLibrary(lib, library, name);
       }
     } catch (err2) {
       exitOnSyncError(err2);
@@ -4120,16 +4248,16 @@ function makeLibraryCommand() {
     "With --create-repo: create the repo private (the store only accepts public repos)"
   ).option("--ref <gitref>", "Git ref to ingest (default: the library branch or main)").option("--dry-run", "Print the plan; push nothing and call no store endpoint").action(
     async (lib, opts) => {
-      const { runLibraryPublish } = await import('../library-publish-FGXF5TJO.js');
+      const { runLibraryPublish } = await import('../library-publish-PICMDSB2.js');
       await withStoreErrorHandling(() => runLibraryPublish(lib, opts));
     }
   );
   cmd.command("register <lib>").description("Register the library's manifest without pushing (bytes already on github)").option("--asset <ref>", "Publish only the single asset matching this ref/name").option("--ref <gitref>", "Git ref to ingest (default: the library branch or main)").option("--dry-run", "Print the plan; call no store endpoint").action(async (lib, opts) => {
-    const { runLibraryRegister } = await import('../library-publish-FGXF5TJO.js');
+    const { runLibraryRegister } = await import('../library-publish-PICMDSB2.js');
     await withStoreErrorHandling(() => runLibraryRegister(lib, opts));
   });
   cmd.command("yank <lib>").description("Retract the library's published assets from the store").option("--asset <ref>", "Yank only the single asset matching this ref/name").action(async (lib, opts) => {
-    const { runLibraryYank } = await import('../library-publish-FGXF5TJO.js');
+    const { runLibraryYank } = await import('../library-publish-PICMDSB2.js');
     await withStoreErrorHandling(() => runLibraryYank(lib, opts));
   });
   return cmd;
@@ -4789,7 +4917,7 @@ function scheduleSoftDepPreview() {
 }
 async function loadAssets() {
   softDepPreviewCache.clear();
-  const { gatherAssetFeeds } = await import('../asset-feeds-K36CR52Q.js');
+  const { gatherAssetFeeds } = await import('../asset-feeds-EYRZR4K5.js');
   const { entries, notes } = await gatherAssetFeeds(am, am.projectDir);
   if (notes.length > 0) {
     state.message = notes.map((n) => `[${n.feed}] ${n.message}`).join(" \u2022 ");
@@ -4976,7 +5104,7 @@ function reconcileCollapsedSets(rows) {
 async function loadSourcesAndLibraries() {
   try {
     const [{ openLibraryManager: openLibraryManager2 }, { getGlobalCacheDir: getGlobalCacheDir2, globalSkaileDir: globalSkaileDir2 }] = await Promise.all([
-      import('../open-library-P3D337NH.js'),
+      import('../open-library-OG457THY.js'),
       import('../core/index.js')
     ]);
     const { manager, library, close } = await openLibraryManager2();
@@ -5349,12 +5477,21 @@ async function applyChanges() {
   render();
   let added = 0;
   let removed = 0;
+  let pruned = 0;
   const appliedAdds = [];
   const appliedRemoves = [];
   for (const ref of state.pendingRemoves) {
-    if (am.remove(ref)) {
-      removed++;
-      appliedRemoves.push(ref);
+    try {
+      const result = await am.removeWithDependencies(ref);
+      if (result.changed) {
+        removed++;
+        pruned += result.pruned.length;
+        appliedRemoves.push(ref);
+      }
+    } catch (err2) {
+      state.message = pc5.red(
+        `Failed to remove ${ref}: ${err2 instanceof Error ? err2.message : err2}`
+      );
     }
   }
   for (const ref of state.pendingAdds) {
@@ -5372,6 +5509,7 @@ async function applyChanges() {
   const parts = [];
   if (added > 0) parts.push(pc5.green(`+${added} added`));
   if (removed > 0) parts.push(pc5.red(`-${removed} removed`));
+  if (pruned > 0) parts.push(pc5.red(`-${pruned} no longer required`));
   const softDeps = appliedAdds.length > 0 ? await am.reportSoftDeps(appliedAdds) : [];
   if (softDeps.length > 0) {
     parts.push(pc5.dim(`${softDeps.length} soft dep${softDeps.length === 1 ? "" : "s"} referenced`));
@@ -5411,7 +5549,10 @@ async function showInfo() {
   console.log(`  installed:   ${row.installed ? pc5.green("yes") : pc5.red("no")}`);
   if (e.requires.length) {
     console.log(`  requires:`);
-    for (const d of e.requires) console.log(`    ${kindColor(d.kind)}:${d.name}`);
+    for (const d of e.requires) {
+      const scope = d.publisher ? `@${d.publisher}/` : "";
+      console.log(`    ${kindColor(d.kind)}:${scope}${d.name}`);
+    }
   }
   if (e.dependencies.length) {
     console.log(`  dependencies:`);
@@ -6422,7 +6563,7 @@ function parseManifestCandidate(c, absRoot) {
   return {
     kind: "value",
     parsed: res.data,
-    body: c.filePath.endsWith(".md") ? parseFrontmatter(content).body : void 0
+    body: readAssetBody(c.filePath, content)
   };
 }
 var PSEUDO_COMPOSE_KINDS = /* @__PURE__ */ new Set(["soul"]);
@@ -6513,6 +6654,7 @@ function validateManifests(rootPath, strictConformance) {
   const candidates = findManifestCandidates(absRoot);
   let errors = 0;
   let warnings = 0;
+  const seenIdentity = /* @__PURE__ */ new Map();
   for (const c of candidates) {
     const parseResult = parseManifestCandidate(c, absRoot);
     if (parseResult.kind === "error") {
@@ -6529,6 +6671,21 @@ function validateManifests(rootPath, strictConformance) {
     );
     errors += delta.errors;
     warnings += delta.warnings;
+    const obj = parseResult.parsed;
+    const identity = obj && typeof obj === "object" ? obj[c.kind === "flow" ? "id" : "name"] : null;
+    if (typeof identity === "string" && identity.length > 0) {
+      const dir = path23__default.dirname(c.filePath);
+      const key = `${c.kind}:${identity}`;
+      const first = seenIdentity.get(key);
+      if (first === void 0) {
+        seenIdentity.set(key, dir);
+      } else if (first !== dir) {
+        logErr(
+          `${path23__default.relative(absRoot, c.filePath)} [${c.kind}] \u2014 ${key} is also defined in ${path23__default.relative(absRoot, first) || "."}; two directories cannot share a kind and name (\`skaile library index\` keeps only the first).`
+        );
+        errors++;
+      }
+    }
   }
   return { total: candidates.length, errors, warnings };
 }
@@ -6667,7 +6824,12 @@ function validatePublishManifestVersions(rootPath) {
     const fileVersion = declaredVersion(res.data);
     if (fileVersion === void 0 || fileVersion === a.version) continue;
     logWarn(
-      `${SKAILE_MANIFEST_FILENAME} [assets] \u2014 ${assetEntryRef(a, manifest)}: manifest version ${a.version} differs from ${toPosix(path23__default.relative(absRoot, file))} (${fileVersion}). The file is the source of truth: bump the version there, then run \`skaile library index <library>\`.`
+      manifestVersionMismatchMessage(
+        assetEntryRef(a, manifest),
+        a.version,
+        toPosix(path23__default.relative(absRoot, file)),
+        fileVersion
+      )
     );
     warnings++;
   }
@@ -6958,6 +7120,7 @@ function makeValidateCommand() {
     const totalErrors = errors + ws.errors + rootErrors + requiresErrors;
     console.log();
     warnIgnoredDomainFiles(absPath);
+    warnLegacyBundleFiles(absPath);
     logInfo(`Scanned ${total} asset manifest(s) and ${ws.total} skaile.yaml file(s)`);
     const totalWarnings = warnings + versionWarnings + publisherWarnings;
     if (totalWarnings > 0) logWarn(`${totalWarnings} warning(s)`);
@@ -8500,6 +8663,7 @@ function resolveSkillName(clonePath, requested) {
   return requested;
 }
 function outdatedRef(e) {
+  if (!e.kind) return e.name;
   const publisher = e.publisher?.replace(/^@/, "");
   return publisher ? `${e.kind}:@${publisher}/${e.name}` : `${e.kind}:${e.name}`;
 }
@@ -8545,9 +8709,9 @@ function makeOutdatedCommand() {
     }
     console.log();
     if (filtered.some((e) => e.problem === void 0)) {
-      logWarn(`Run ${S.cmd("skaile update")} to re-deploy.`);
+      logWarn(`Run ${S.cmd("skaile update")} to re-lock and re-deploy.`);
     }
-    if (filtered.some((e) => e.problem !== void 0)) {
+    if (filtered.some((e) => e.problem !== void 0 && !e.manualFix)) {
       logWarn(`Run ${S.cmd("skaile install")} to restore or re-lock the broken assets.`);
     }
   });
@@ -8620,7 +8784,7 @@ function action2(fn) {
   };
 }
 async function reconcileAndReport(projectDir, plugins) {
-  const { reconcilePlugins } = await import('../plugin-store-WI4MZJLP.js');
+  const { reconcilePlugins } = await import('../plugin-store-MPAMD5OT.js');
   if (plugins.length === 0) {
     logInfo("No plugins declared \u2014 nothing to reconcile.");
     return;
@@ -8636,7 +8800,7 @@ async function reconcileAndReport(projectDir, plugins) {
 async function runInstall2(spec, opts) {
   const projectDir = path23__default.resolve(opts.projectDir);
   const { WorkspaceYamlEditor: WorkspaceYamlEditor2 } = await import('../core/index.js');
-  const { specName } = await import('../plugin-store-WI4MZJLP.js');
+  const { specName } = await import('../plugin-store-MPAMD5OT.js');
   const yamlPath = path23__default.join(projectDir, "skaile.yaml");
   const editor = WorkspaceYamlEditor2.load(yamlPath);
   const replaced = editor.addPlugin(spec, specName);
@@ -8648,7 +8812,7 @@ async function runInstall2(spec, opts) {
 async function runRemove(name, opts) {
   const projectDir = path23__default.resolve(opts.projectDir);
   const { WorkspaceYamlEditor: WorkspaceYamlEditor2 } = await import('../core/index.js');
-  const { specName } = await import('../plugin-store-WI4MZJLP.js');
+  const { specName } = await import('../plugin-store-MPAMD5OT.js');
   const yamlPath = path23__default.join(projectDir, "skaile.yaml");
   const editor = WorkspaceYamlEditor2.load(yamlPath);
   const removed = editor.removePlugin(name, specName);
@@ -8676,7 +8840,7 @@ async function runList(opts) {
   const registry = createPluginRegistry();
   if (declared.length > 0) {
     try {
-      const { loadPlugins } = await import('../plugin-store-WI4MZJLP.js');
+      const { loadPlugins } = await import('../plugin-store-MPAMD5OT.js');
       const result = await loadPlugins(projectDir, declared, registry);
       for (const f of result.failed) logWarn(f.error);
     } catch (err2) {
@@ -9893,12 +10057,12 @@ function makeServeCommand() {
   );
 }
 async function ensurePluginsLoadedForServe(projectDir) {
-  const { logInfo: logInfo2, logWarn: logWarn2 } = await import('../helpers-KC5O7CML.js');
+  const { logInfo: logInfo2, logWarn: logWarn2 } = await import('../helpers-MWZDRBLD.js');
   try {
     const { resolveSkWorkspaceConfig: resolveSkWorkspaceConfig2 } = await import('../core/index.js');
     const config = resolveSkWorkspaceConfig2(projectDir);
     if (!config.plugins || config.plugins.length === 0) return;
-    const { ensurePluginsLoaded } = await import('../plugin-store-WI4MZJLP.js');
+    const { ensurePluginsLoaded } = await import('../plugin-store-MPAMD5OT.js');
     const { pluginRegistry } = await import('../plugin-registry/index.js');
     const result = await ensurePluginsLoaded(projectDir, config.plugins, pluginRegistry);
     if (result.loaded.length > 0) {
@@ -9912,14 +10076,14 @@ async function ensurePluginsLoadedForServe(projectDir) {
   }
 }
 async function runCompileTest(opts) {
-  const { logOk: logOk2, logErr: logErr2, logInfo: logInfo2, S: S2 } = await import('../helpers-KC5O7CML.js');
+  const { logOk: logOk2, logErr: logErr2, logInfo: logInfo2, S: S2 } = await import('../helpers-MWZDRBLD.js');
   const { tmpdir } = await import('os');
   const { dirname: dirname3, join: join7, resolve: resolve5 } = await import('path');
   const { fileURLToPath: fileURLToPath2 } = await import('url');
   const { unlinkSync, existsSync: existsSync18 } = await import('fs');
   const { spawn } = await import('child_process');
   const { portableSpawnSync: portableSpawnSync2 } = await import('../core/index.js');
-  const { MONOREPO_ROOT } = await import('../paths-JKEKXM52.js');
+  const { MONOREPO_ROOT } = await import('../paths-FQ64OLJG.js');
   if (MONOREPO_ROOT === null) {
     logErr2("--compile-test is only available inside the skaile-dev workspace.");
     logInfo2("Run it from a checkout of skaile-ai/skaile-dev (the monorepo shell).");
@@ -10655,11 +10819,19 @@ function makeSessionCommand() {
   });
   cmd.command("switch <run-id>").description("Switch the current session").option("--project-dir <path>", "Project directory", process.cwd()).action(async (runId, opts) => {
     const projectDir = path23__default.resolve(opts.projectDir);
+    if (!await loadSessionById(projectDir, runId)) {
+      logErr(`Session not found: ${runId}`);
+      process.exit(1);
+    }
     await setCurrentSession(projectDir, runId);
     logOk(`Switched to session: ${S.dim(runId.slice(0, 8))}`);
   });
   cmd.command("delete <run-id>").description("Delete a session").option("--project-dir <path>", "Project directory", process.cwd()).action(async (runId, opts) => {
     const projectDir = path23__default.resolve(opts.projectDir);
+    if (!await loadSessionById(projectDir, runId)) {
+      logErr(`Session not found: ${runId}`);
+      process.exit(1);
+    }
     await deleteSession(projectDir, runId);
     logOk(`Deleted session: ${S.dim(runId.slice(0, 8))}`);
   });
@@ -10796,7 +10968,7 @@ function makeStoreCommand() {
     process.exit(2);
   });
   store.command("search <query>").description("Search the AI Asset Store catalog by name, description, or publisher").option("--kind <kind>", "Filter by asset kind (skill, agent, prompt, flow, \u2026)").option("-C, --project-dir <dir>", "Project directory (catalog config overlay)", process.cwd()).action(async (query, opts) => {
-    const { openCatalogSource: openCatalogSource2, LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-P3D337NH.js');
+    const { openCatalogSource: openCatalogSource2, LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-OG457THY.js');
     try {
       const remote = await openCatalogSource2({ projectDir: path23__default.resolve(opts.projectDir) });
       const assets = await remote.listAssets(opts.kind ? { kind: opts.kind } : {});
@@ -10824,8 +10996,8 @@ function makeStoreCommand() {
     }
   });
   store.command("show <ref>").description("Show a store asset's details + provenance (source, files, integrity)").option("-C, --project-dir <dir>", "Project directory (catalog config overlay)", process.cwd()).action(async (ref, opts) => {
-    const { openCatalogSource: openCatalogSource2, LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-P3D337NH.js');
-    const { supportsInstallManifest } = await import('../project-WFUDVYNN.js');
+    const { openCatalogSource: openCatalogSource2, LocalCatalogDisabledError: LocalCatalogDisabledError2 } = await import('../open-library-OG457THY.js');
+    const { supportsInstallManifest } = await import('../project-2GFT5LEZ.js');
     try {
       const remote = await openCatalogSource2({ projectDir: path23__default.resolve(opts.projectDir) });
       const asset = await remote.resolve(ref);
@@ -10938,14 +11110,15 @@ function makeStoreCommand() {
   });
   return store;
 }
-function printTree(node, prefix = "", isLast = true) {
-  const connector = prefix === "" ? "" : isLast ? "\u2514\u2500 " : "\u251C\u2500 ";
-  const line = prefix + connector + colorRef(node.ref);
-  console.log(`  ${line}`);
-  const childPrefix = prefix + (prefix === "" ? "" : isLast ? "   " : "\u2502  ");
-  for (let i = 0; i < node.children.length; i++) {
-    printTree(node.children[i], childPrefix, i === node.children.length - 1);
-  }
+function printChildren(nodes, prefix) {
+  nodes.forEach((node, i) => {
+    const isLast = i === nodes.length - 1;
+    console.log(`  ${prefix}${isLast ? "\u2514\u2500 " : "\u251C\u2500 "}${colorRef(node.ref)}`);
+    printChildren(node.children, prefix + (isLast ? "   " : "\u2502  "));
+  });
+}
+function treeRefs(nodes) {
+  return [...new Set(nodes.flatMap((n) => [n.ref, ...treeRefs(n.children)]))];
 }
 function makeTreeCommand() {
   return new Command("tree").description("Show full dependency tree").option("--project-dir <path>", "Project directory", process.cwd()).action(async (opts) => {
@@ -10953,14 +11126,15 @@ function makeTreeCommand() {
       registry: getKindRegistry(),
       projectDir: path23__default.resolve(opts.projectDir)
     });
-    const root = am2.tree();
+    const root = await am2.tree();
     if (root.children.length === 0) {
       logInfo("No dependencies in lock file. Run `skaile install` first.");
       return;
     }
     console.log();
-    printTree(root);
-    const softDeps = await am2.softDepsOf(root.children.map((c) => c.ref));
+    console.log(`  ${colorRef(root.ref)}`);
+    printChildren(root.children, "");
+    const softDeps = await am2.softDepsOf(treeRefs(root.children));
     if (softDeps.length > 0) {
       console.log(`  ${S.label("Soft dependencies (inferred)")}:`);
       for (const e of softDeps)
@@ -11003,6 +11177,7 @@ function makeUpdateCommand() {
         syncSpinner.stop(
           total === 0 ? "No sources to sync." : `Synced ${S.heading(`${synced}/${total}`)} source(s)` + (failed ? ` (${failed} failed)` : "")
         );
+        if (failed > 0) process.exitCode = 1;
       }
       const warnings = deferredWarnings();
       const am2 = new AssetManager({
@@ -11025,7 +11200,17 @@ function makeUpdateCommand() {
       warnings.flush();
       if (result.deployed.length > 0) {
         for (const d of result.deployed) logOk(`Updated ${d}`);
-      } else {
+      }
+      for (const r of result.removed) logWarn(`Removed: ${r}`);
+      reportRelocked(result.relocked);
+      const changed = result.deployed.length > 0 || result.removed.length > 0 || !!result.relocked?.length;
+      if (result.lockWritten && changed) {
+        logInfo(`Lock file written: ${S.dim("skaile.lock.yaml")}`);
+      }
+      if (result.missing.length > 0) {
+        for (const m of result.missing) logErr(`Missing: ${m}${result.missingHints?.[m] ?? ""}`);
+        process.exitCode = 1;
+      } else if (!changed) {
         logInfo("Nothing to update.");
       }
     }
@@ -11141,7 +11326,7 @@ function makeWhyCommand() {
       registry: getKindRegistry(),
       projectDir: path23__default.resolve(opts.projectDir)
     });
-    const chain = am2.why(ref);
+    const chain = await am2.why(ref);
     if (chain.length === 0) {
       let declared;
       try {
@@ -11426,7 +11611,7 @@ async function bootstrapUserConfig() {
 }
 async function hydrateInitSources(resolved, created) {
   try {
-    const { ensureSourcesCloned } = await import('../ensure-sources-277VI7R3.js');
+    const { ensureSourcesCloned } = await import('../ensure-sources-SKLNM4UZ.js');
     const hydrate = ensureSourcesCloned(resolved, { quiet: true });
     for (const n of hydrate.cloned) created.push(`~/.skaile/cache/sources/${n}/`);
     if (hydrate.failed.length > 0) {
@@ -11466,7 +11651,7 @@ function printInitSummary(resolved, projectDir, created) {
   console.log();
 }
 program.command("setup").description("Interactive provider setup wizard").action(async () => {
-  const { cmdSetup } = await import('../setup-RAMLTORM.js');
+  const { cmdSetup } = await import('../setup-WHMCSIF2.js');
   await cmdSetup([], { projectDir: process.cwd() });
 });
 program.addCommand(makeInstallCommand());