@pkgseer/cli 0.5.0 → 0.5.2

package/dist/cli.js

@@ -1,7 +1,7 @@
 #!/usr/bin/env node
 import {
   version
-} from "./shared/chunk-kh5enjt9.js";
+} from "./shared/chunk-a0vv3x03.js";
 
 // src/cli.ts
 import { Command } from "commander";
@@ -335,6 +335,8 @@ var FetchCodeContextDocument = gql`
     endLine
     repoUrl
     gitRef
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -363,6 +365,16 @@ var TriggerIndexingDocument = gql`
   }
 }
     `;
+var IndexingProgressDocument = gql`
+    query IndexingProgress($ref: String!) {
+  indexingProgress(ref: $ref) {
+    status
+    filesIndexed
+    chunksCreated
+    elapsedMs
+  }
+}
+    `;
 var CreateProjectDocument = gql`
     mutation CreateProject($input: CreateProjectInput!) {
   createProject(input: $input) {
@@ -699,6 +711,8 @@ var FindSymbolDocument = gql`
       indexedAt
       hint
     }
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -747,6 +761,8 @@ var SearchSymbolsDocument = gql`
       hint
     }
     warning
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -786,6 +802,8 @@ var ListSymbolsDocument = gql`
       path
       language
     }
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -825,6 +843,8 @@ var SymbolDependenciesDocument = gql`
     missingPackages
     total
     hasMore
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -854,6 +874,8 @@ var SymbolDependentsDocument = gql`
     }
     total
     hasMore
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -888,6 +910,8 @@ var PackageImportsDocument = gql`
     }
     uniqueDependencies
     unresolvedCount
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -921,6 +945,8 @@ var CallPathDocument = gql`
         callLine
       }
     }
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -981,6 +1007,8 @@ var ListRepoFilesDocument = gql`
       indexedAt
       hint
     }
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -1017,6 +1045,8 @@ var GrepRepoFileDocument = gql`
       indexedAt
       hint
     }
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -1074,6 +1104,8 @@ var VersionDiffDocument = gql`
       }
     }
     hasMore
+    indexingStatus
+    indexingRef
   }
 }
     `;
@@ -1092,6 +1124,7 @@ var SearchResultsDocumentString = print(SearchResultsDocument);
 var FetchCodeContextDocumentString = print(FetchCodeContextDocument);
 var CliDocsGetDocumentString = print(CliDocsGetDocument);
 var TriggerIndexingDocumentString = print(TriggerIndexingDocument);
+var IndexingProgressDocumentString = print(IndexingProgressDocument);
 var CreateProjectDocumentString = print(CreateProjectDocument);
 var PackageSummaryDocumentString = print(PackageSummaryDocument);
 var PackageVulnerabilitiesDocumentString = print(PackageVulnerabilitiesDocument);
@@ -1157,6 +1190,9 @@ function getSdk(client, withWrapper = defaultWrapper) {
     TriggerIndexing(variables, requestHeaders) {
       return withWrapper((wrappedRequestHeaders) => client.rawRequest(TriggerIndexingDocumentString, variables, { ...requestHeaders, ...wrappedRequestHeaders }), "TriggerIndexing", "mutation", variables);
     },
+    IndexingProgress(variables, requestHeaders) {
+      return withWrapper((wrappedRequestHeaders) => client.rawRequest(IndexingProgressDocumentString, variables, { ...requestHeaders, ...wrappedRequestHeaders }), "IndexingProgress", "query", variables);
+    },
     CreateProject(variables, requestHeaders) {
       return withWrapper((wrappedRequestHeaders) => client.rawRequest(CreateProjectDocumentString, variables, { ...requestHeaders, ...wrappedRequestHeaders }), "CreateProject", "mutation", variables);
     },
@@ -1671,6 +1707,7 @@ var TOOL_NAMES = [
   "list_imports",
   "call_path",
   "trigger_indexing",
+  "indexing_status",
   "version_diff"
 ];
 var TOOL_NAME_MIGRATION = {
@@ -2405,6 +2442,10 @@ class PkgseerServiceImpl {
     });
     return { data: result.data, errors: result.errors };
   }
+  async getIndexingProgress(ref) {
+    const result = await this.client.IndexingProgress({ ref });
+    return { data: result.data, errors: result.errors };
+  }
   async triggerIndexing(input) {
     const result = await this.client.TriggerIndexing({ input });
     return { data: result.data, errors: result.errors };
@@ -2822,6 +2863,14 @@ function handleErrors(errors, json) {
   const hint = CLI_HINTS[classifyError(combined)];
   outputError(`${combined}${hint}`, json);
 }
+function handleIndexingInProgress(data, json) {
+  if (data.indexingStatus === "INDEXING") {
+    const refInfo = data.indexingRef ? ` (ref: ${data.indexingRef})` : "";
+    outputError(`Target is being indexed${refInfo}. Retry with a longer --wait value or try again later.`, json);
+    return true;
+  }
+  return false;
+}
 function formatNumber(num) {
   if (num == null)
     return "N/A";
@@ -3036,7 +3085,8 @@ function formatDependencyEntry(entry) {
 // src/commands/code/callees.ts
 function formatCalleesResult(data) {
   const lines = [];
-  lines.push(`Callees of ${data.root.qualifiedPath ?? data.root.name} (ref:${data.root.symbolRef})`);
+  const rootLabel = data.root ? `${data.root.qualifiedPath ?? data.root.name} (ref:${data.root.symbolRef})` : "unknown";
+  lines.push(`Callees of ${rootLabel}`);
   lines.push(`${data.total} callee(s)${data.hasMore ? " (more available)" : ""}`);
   if (data.externalPackages && data.externalPackages.length > 0) {
     lines.push(`External packages: ${data.externalPackages.join(", ")}`);
@@ -3067,10 +3117,13 @@ async function codeCalleesAction(symbolArg, options, deps) {
     waitTimeoutMs: parseWaitTimeout(options.wait)
   });
   handleErrors(result.errors, options.json ?? false);
+  const data = result.data.symbolDependencies;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
-    output(result.data.symbolDependencies, true);
+    output(data, true);
   } else {
-    console.log(formatCalleesResult(result.data.symbolDependencies));
+    console.log(formatCalleesResult(data));
   }
 }
 var CALLEES_DESCRIPTION = `Find what a symbol calls.
@@ -3093,7 +3146,8 @@ function registerCodeCalleesCommand(program) {
 // src/commands/code/callers.ts
 function formatCallersResult(data) {
   const lines = [];
-  lines.push(`Callers of ${data.target.qualifiedPath ?? data.target.name} (ref:${data.target.symbolRef})`);
+  const targetLabel = data.target ? `${data.target.qualifiedPath ?? data.target.name} (ref:${data.target.symbolRef})` : "unknown";
+  lines.push(`Callers of ${targetLabel}`);
   lines.push(`${data.total} caller(s)${data.hasMore ? " (more available)" : ""}`);
   lines.push("");
   for (const dep of data.dependents) {
@@ -3114,10 +3168,13 @@ async function codeCallersAction(symbolArg, options, deps) {
     waitTimeoutMs: parseWaitTimeout(options.wait)
   });
   handleErrors(result.errors, options.json ?? false);
+  const data = result.data.symbolDependents;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
-    output(result.data.symbolDependents, true);
+    output(data, true);
   } else {
-    console.log(formatCallersResult(result.data.symbolDependents));
+    console.log(formatCallersResult(data));
   }
 }
 var CALLERS_DESCRIPTION = `Find what calls a symbol.
@@ -3140,12 +3197,14 @@ function registerCodeCallersCommand(program) {
 // src/commands/code/diff.ts
 function formatDiffResult(data) {
   const lines = [];
-  lines.push(`Version diff: ${data.fromVersion} → ${data.toVersion}`);
+  lines.push(`Version diff: ${data.fromVersion ?? "unknown"} → ${data.toVersion ?? "unknown"}`);
   lines.push("");
-  const s = data.summary;
-  lines.push("Summary:");
-  lines.push(`  Added: ${s.added}  Removed: ${s.removed}  Modified: ${s.modified}  Moved: ${s.moved}`);
-  lines.push(`  Breaking: ${s.breaking}  Behavior changes: ${s.behaviorChange}`);
+  if (data.summary) {
+    const s = data.summary;
+    lines.push("Summary:");
+    lines.push(`  Added: ${s.added}  Removed: ${s.removed}  Modified: ${s.modified}  Moved: ${s.moved}`);
+    lines.push(`  Breaking: ${s.breaking}  Behavior changes: ${s.behaviorChange}`);
+  }
   if (data.hasMore) {
     lines.push("  (more changes available, increase --limit)");
   }
@@ -3182,10 +3241,13 @@ async function codeDiffAction(packageArg, fromVersion, toVersion, options, deps)
     waitTimeoutMs: parseWaitTimeout(options.wait)
   });
   handleErrors(result.errors, options.json ?? false);
+  const data = result.data.versionDiff;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
-    output(result.data.versionDiff, true);
+    output(data, true);
   } else {
-    console.log(formatDiffResult(result.data.versionDiff));
+    console.log(formatDiffResult(data));
   }
 }
 var DIFF_DESCRIPTION = `Compare symbols between two package versions.
@@ -3239,6 +3301,8 @@ async function codeFilesAction(packageArg, options, deps) {
   });
   handleErrors(result.errors, options.json ?? false);
   const data = result.data.listRepoFiles;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
     output(data, true);
   } else {
@@ -3300,6 +3364,8 @@ async function codeFindAction(packageArg, nameArg, options, deps) {
   });
   handleErrors(result.errors, options.json ?? false);
   const data = result.data.findSymbol;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
     output(data, true);
   } else {
@@ -3370,6 +3436,8 @@ async function codeGrepAction(packageArg, filePath, pattern, options, deps) {
   });
   handleErrors(result.errors, options.json ?? false);
   const data = result.data.grepRepoFile;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
     output(data, true);
   } else {
@@ -3452,10 +3520,13 @@ async function codeImportsAction(packageArg, options, deps) {
     waitTimeoutMs: parseWaitTimeout(options.wait)
   });
   handleErrors(result.errors, options.json ?? false);
+  const data = result.data.packageImports;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
-    output(result.data.packageImports, true);
+    output(data, true);
   } else {
-    console.log(formatImportsResult(result.data.packageImports));
+    console.log(formatImportsResult(data));
   }
 }
 var IMPORTS_DESCRIPTION = `List import statements in a package.
@@ -3517,10 +3588,13 @@ async function codeListAction(packageArg, options, deps) {
     waitTimeoutMs: parseWaitTimeout(options.wait)
   });
   handleErrors(result.errors, options.json ?? false);
+  const data = result.data.listSymbols;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
-    output(result.data.listSymbols, true);
+    output(data, true);
   } else {
-    console.log(formatListResult(result.data.listSymbols));
+    console.log(formatListResult(data));
   }
 }
 var LIST_DESCRIPTION = `Browse symbols in a package.
@@ -3544,8 +3618,8 @@ function registerCodeListCommand(program) {
 // src/commands/code/path.ts
 function formatPathResult(data) {
   const lines = [];
-  const fromName = data.fromSymbol.qualifiedPath ?? data.fromSymbol.name;
-  const toName = data.toSymbol.qualifiedPath ?? data.toSymbol.name;
+  const fromName = data.fromSymbol ? data.fromSymbol.qualifiedPath ?? data.fromSymbol.name : "unknown";
+  const toName = data.toSymbol ? data.toSymbol.qualifiedPath ?? data.toSymbol.name : "unknown";
   lines.push(`Call path: ${fromName} -> ${toName}`);
   if (!data.pathFound) {
     lines.push("No path found between these symbols.");
@@ -3578,10 +3652,13 @@ async function codePathAction(fromArg, toArg, options, deps) {
     waitTimeoutMs: parseWaitTimeout(options.wait)
   });
   handleErrors(result.errors, options.json ?? false);
+  const data = result.data.callPath;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
-    output(result.data.callPath, true);
+    output(data, true);
   } else {
-    console.log(formatPathResult(result.data.callPath));
+    console.log(formatPathResult(data));
   }
 }
 var PATH_DESCRIPTION = `Find call path between two symbols.
@@ -3655,6 +3732,8 @@ async function codeSearchAction(packageArg, query, options, deps) {
   });
   handleErrors(result.errors, options.json ?? false);
   const data = result.data.searchSymbols;
+  if (handleIndexingInProgress(data, options.json ?? false))
+    return;
   if (options.json) {
     output(data, true);
   } else {
@@ -6804,7 +6883,7 @@ var schemas = {
   packageName: z2.string().max(255).describe("Name of the package"),
   version: z2.string().max(100).optional().describe("Specific version, e.g. '4.18.2' (defaults to latest)"),
   navigationMode: z2.enum(["summary", "detailed"]).optional().describe("Response detail level. summary (default) returns core fields; detailed adds all optional fields."),
-  waitTimeoutMs: z2.coerce.number().int().min(0).max(30000).optional().describe("Max milliseconds to wait for package indexing (0-30000, default 10000). Set 0 to error immediately if not indexed."),
+  waitTimeoutMs: z2.coerce.number().int().min(0).max(60000).optional().describe("Max milliseconds to wait for indexing (0-60000, default 10000). Set 0 to error immediately if not indexed."),
   symbolReference: z2.object({
     symbol_ref: z2.string().optional().describe("Compound symbol reference (registry:package:version:id) from find_symbol or list_symbols results. Self-contained — no additional fields needed."),
     registry: z2.enum(["npm", "pypi", "hex", "crates", "nuget", "maven", "zig", "vcpkg"]).optional().describe("Package registry. For package-scoped lookup (with package_name + symbol_name)."),
@@ -6893,7 +6972,7 @@ function buildCodeTargetVars(resolved) {
 }
 var DEFAULT_WAIT_TIMEOUT_MS2 = 1e4;
 var MCP_HINTS = {
-  being_indexed: "Hint: package is being indexed. Try again with a longer wait_timeout_ms (e.g., 30000).",
+  being_indexed: "Hint: target is being indexed. Retry with a longer wait_timeout_ms (e.g., 30000) or use indexing_status to poll progress.",
   timeout: "Hint: this may be transient — retry the same query. If the issue persists, try simplifying the query."
 };
 function buildHintedMessage(operation, message) {
@@ -6922,14 +7001,50 @@ function buildHintedMessage(operation, message) {
   return `Failed to ${operation}: ${message}`;
 }
 var MCP_GRAPHQL_HINTS = {
-  not_found: "Hint: verify the package name and registry are correct.",
-  being_indexed: "Hint: package is being indexed. Try again with a longer wait_timeout_ms (e.g., 30000).",
+  not_found: "Hint: verify the package name, registry, or repository URL are correct.",
+  being_indexed: "Hint: target is being indexed. Retry with a longer wait_timeout_ms (e.g., 30000) or use indexing_status to poll progress.",
   timeout: "Hint: this may be transient — retry the same query. If the issue persists, try simplifying the query."
 };
+function getExtensionCode(errors) {
+  for (const error2 of errors) {
+    const ext = error2.extensions;
+    if (ext?.code && typeof ext.code === "string") {
+      return ext.code;
+    }
+  }
+  return;
+}
+function getExtensionIndexingRef(errors) {
+  for (const error2 of errors) {
+    const ext = error2.extensions;
+    const ref = ext?.indexing_ref ?? ext?.indexingRef;
+    if (ref && typeof ref === "string") {
+      return ref;
+    }
+  }
+  return;
+}
+var EXTENSION_CODE_HINTS = {
+  PACKAGE_INDEXING: "Hint: target is being indexed. Use indexing_status to poll progress, or retry with a longer wait_timeout_ms.",
+  NOT_FOUND: "Hint: verify the package name, registry, or repository URL are correct."
+};
 function handleGraphQLErrors(errors) {
   if (errors && errors.length > 0) {
     const combined = errors.map((e) => e.message).filter(Boolean).join(", ");
-    const hint = MCP_GRAPHQL_HINTS[classifyError(combined)];
+    const extensionCode = getExtensionCode(errors);
+    const indexingRef = getExtensionIndexingRef(errors);
+    if (extensionCode === "PACKAGE_INDEXING" && indexingRef) {
+      return errorResult(JSON.stringify({
+        error: combined,
+        indexingStatus: "INDEXING",
+        indexingRef,
+        message: "Target is being indexed. Use indexing_status tool with this indexingRef to poll progress, " + "or retry the original query after indexing completes."
+      }));
+    }
+    if (extensionCode === "PACKAGE_INDEXING") {
+      return errorResult(`Error: ${combined}. ` + "Hint: target is being indexed (background refresh). Retry the query in a few seconds.");
+    }
+    const hint = extensionCode ? EXTENSION_CODE_HINTS[extensionCode] : MCP_GRAPHQL_HINTS[classifyError(combined)];
     const suffix = hint ? `. ${hint}` : "";
     return errorResult(`Error: ${combined}${suffix}`);
   }
@@ -6943,6 +7058,19 @@ async function withErrorHandling(operation, fn) {
     return errorResult(buildHintedMessage(operation, message));
   }
 }
+function handleIndexingStatus(data) {
+  if (data.indexingStatus === "INDEXING") {
+    const response = {
+      indexingStatus: "INDEXING",
+      message: "Target is being indexed. Use indexing_status tool with this indexingRef to poll progress, " + "or retry the original query after indexing completes."
+    };
+    if (data.indexingRef) {
+      response.indexingRef = data.indexingRef;
+    }
+    return errorResult(JSON.stringify(response));
+  }
+  return null;
+}
 function notFoundError(packageName, registry) {
   return errorResult(`Package not found: ${packageName} in ${registry}. Verify the package name and registry are correct.`);
 }
@@ -6979,7 +7107,11 @@ function createCallPathTool(pkgseerService) {
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
-        return textResult(JSON.stringify(result.data.callPath, null, 2));
+        const data = result.data.callPath;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
+        return textResult(JSON.stringify(data, null, 2));
       });
     }
   };
@@ -7094,6 +7226,9 @@ function createFindSymbolTool(pkgseerService) {
         if (graphqlError)
           return graphqlError;
         const data = result.data.findSymbol;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
         if (data.symbols.length === 0 && data.diagnostics?.hint) {
           return textResult(JSON.stringify({ ...data, _hint: data.diagnostics.hint }, null, 2));
         }
@@ -7136,6 +7271,9 @@ function createGrepFileTool(pkgseerService) {
         if (graphqlError)
           return graphqlError;
         const data = result.data.grepRepoFile;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
         if (data.matches.length === 0 && data.diagnostics?.hint) {
           return textResult(JSON.stringify({ ...data, _hint: data.diagnostics.hint }, null, 2));
         }
@@ -7144,19 +7282,67 @@ function createGrepFileTool(pkgseerService) {
     }
   };
 }
-// src/tools/list-files.ts
+// src/tools/indexing-status.ts
 import { z as z8 } from "zod";
 var argsSchema6 = {
+  ref: z8.string().min(1).describe("Indexing reference from a previous tool result (returned when indexing times out).")
+};
+function createIndexingStatusTool(pkgseerService) {
+  return {
+    name: "indexing_status",
+    description: "Check indexing progress for a code navigation target. " + "Use after any code navigation tool returns an indexingRef (when indexing exceeded wait_timeout_ms). " + "Returns status (PENDING, INDEXING, INDEXED, FAILED, NOT_FOUND) with progress details. " + "When status is INDEXED, retry the original query to get results.",
+    schema: argsSchema6,
+    annotations: { readOnlyHint: true },
+    handler: async ({ ref }, _extra) => {
+      return withErrorHandling("check indexing status", async () => {
+        const result = await pkgseerService.getIndexingProgress(ref);
+        const graphqlError = handleGraphQLErrors(result.errors);
+        if (graphqlError)
+          return graphqlError;
+        const progress = result.data?.indexingProgress;
+        if (!progress) {
+          return errorResult("Indexing session not found. The reference may be invalid or the session may have expired.");
+        }
+        const response = {
+          status: progress.status,
+          ref
+        };
+        if (progress.filesIndexed != null) {
+          response.filesIndexed = progress.filesIndexed;
+        }
+        if (progress.chunksCreated != null) {
+          response.chunksCreated = progress.chunksCreated;
+        }
+        if (progress.elapsedMs != null) {
+          response.elapsedMs = progress.elapsedMs;
+        }
+        if (progress.status === "INDEXED") {
+          response.message = "Indexing is complete. Retry your original query to get results.";
+        } else if (progress.status === "INDEXING" || progress.status === "PENDING") {
+          response.message = "Indexing is in progress. Poll again to check status.";
+        } else if (progress.status === "FAILED") {
+          response.message = "Indexing failed.";
+        } else if (progress.status === "NOT_FOUND") {
+          response.message = "Indexing reference not found. The ref may be invalid or the session may have expired.";
+        }
+        return textResult(JSON.stringify(response, null, 2));
+      });
+    }
+  };
+}
+// src/tools/list-files.ts
+import { z as z9 } from "zod";
+var argsSchema7 = {
   target: schemas.codeTarget,
-  path_prefix: z8.string().optional().describe("Filter to files under this path (e.g., 'src/')"),
-  limit: z8.coerce.number().int().min(1).max(1000).optional().describe("Max files to return (max 1000)"),
+  path_prefix: z9.string().optional().describe("Filter to files under this path (e.g., 'src/')"),
+  limit: z9.coerce.number().int().min(1).max(1000).optional().describe("Max files to return (max 1000)"),
   wait_timeout_ms: schemas.waitTimeoutMs
 };
 function createListFilesTool(pkgseerService) {
   return {
     name: "list_files",
     description: "Explore a dependency's file structure — " + "see what source files, configs, and docs exist. " + "Accepts package scope (registry + package_name) or repo scope (repo_url + git_ref) via the target parameter. " + "Returns file paths, names, languages, types (source/doc/config), and sizes. " + "Use path_prefix to filter by directory (e.g., 'src/'). " + "Good first step when investigating unfamiliar package internals. " + "In monorepos with package scope, returns only files within this package's subdirectory. " + "Requires code indexing.",
-    schema: argsSchema6,
+    schema: argsSchema7,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("list files", async () => {
@@ -7176,6 +7362,9 @@ function createListFilesTool(pkgseerService) {
         if (graphqlError)
           return graphqlError;
         const data = result.data.listRepoFiles;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
         if (data.files.length === 0 && data.diagnostics?.hint) {
           return textResult(JSON.stringify({ ...data, _hint: data.diagnostics.hint }, null, 2));
         }
@@ -7185,12 +7374,12 @@ function createListFilesTool(pkgseerService) {
   };
 }
 // src/tools/list-imports.ts
-import { z as z9 } from "zod";
-var argsSchema7 = {
+import { z as z10 } from "zod";
+var argsSchema8 = {
   target: schemas.codeTarget,
-  file_path: z9.string().max(1000).optional().describe("Filter to a specific file path"),
-  resolved_only: z9.boolean().optional().describe("Only return imports resolved to a known package"),
-  limit: z9.coerce.number().int().min(1).max(500).optional().describe("Max imports to return"),
+  file_path: z10.string().max(1000).optional().describe("Filter to a specific file path"),
+  resolved_only: z10.boolean().optional().describe("Only return imports resolved to a known package"),
+  limit: z10.coerce.number().int().min(1).max(500).optional().describe("Max imports to return"),
   mode: schemas.navigationMode,
   wait_timeout_ms: schemas.waitTimeoutMs
 };
@@ -7198,7 +7387,7 @@ function createListImportsTool(pkgseerService) {
   return {
     name: "list_imports",
     description: "See what a dependency imports — understand its internal dependencies and external package usage. " + "Accepts package scope (registry + package_name) or repo scope (repo_url + git_ref) via the target parameter. " + "Returns parsed import/require/use statements with optional resolution to known packages. " + "Use resolved_only=true to see only imports that map to packages in the PkgSeer registry. " + "Includes: source path, imported names, and de-duplicated dependency list.",
-    schema: argsSchema7,
+    schema: argsSchema8,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("list imports", async () => {
@@ -7219,13 +7408,17 @@ function createListImportsTool(pkgseerService) {
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
-        return textResult(JSON.stringify(result.data.packageImports, null, 2));
+        const data = result.data.packageImports;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
+        return textResult(JSON.stringify(data, null, 2));
       });
     }
   };
 }
 // src/tools/list-package-docs.ts
-var argsSchema8 = {
+var argsSchema9 = {
   registry: schemas.registry,
   package_name: schemas.packageName.describe("Name of the package to list documentation for"),
   version: schemas.version
@@ -7234,7 +7427,7 @@ function createListPackageDocsTool(pkgseerService) {
   return {
     name: "list_package_docs",
     description: "Discover available documentation pages for a package. Start here before fetching or searching docs. " + "Returns: page titles, unique IDs (needed for fetch_package_doc), word counts, and update timestamps. " + "Workflow: list_package_docs → fetch_package_doc for full content, or search(mode='docs') to find specific topics. " + "Requires documentation to have been crawled — if results are empty, use trigger_indexing first, then retry.",
-    schema: argsSchema8,
+    schema: argsSchema9,
     annotations: { readOnlyHint: true },
     handler: async ({ registry, package_name, version: version2 }, _extra) => {
       return withErrorHandling("list package documentation", async () => {
@@ -7251,15 +7444,15 @@ function createListPackageDocsTool(pkgseerService) {
   };
 }
 // src/tools/list-symbols.ts
-import { z as z10 } from "zod";
-var argsSchema9 = {
+import { z as z11 } from "zod";
+var argsSchema10 = {
   target: schemas.codeTarget,
-  scope: z10.enum(["exports", "file"]).describe("Browsing scope: 'exports' for public API, 'file' for all symbols in a specific file"),
-  file_path: z10.string().max(1000).optional().describe("File path within the repo (required when scope=file)"),
-  namespace: z10.string().max(500).optional().describe("Filter by namespace prefix (e.g., 'React' to see React.*)"),
-  public_only: z10.boolean().optional().describe("Only return public symbols"),
-  include_popularity: z10.boolean().optional().describe("Include callerCount for each symbol (slightly slower)"),
-  limit: z10.coerce.number().int().min(1).max(100).optional().describe("Max symbols to return (max 100)"),
+  scope: z11.enum(["exports", "file"]).describe("Browsing scope: 'exports' for public API, 'file' for all symbols in a specific file"),
+  file_path: z11.string().max(1000).optional().describe("File path within the repo (required when scope=file)"),
+  namespace: z11.string().max(500).optional().describe("Filter by namespace prefix (e.g., 'React' to see React.*)"),
+  public_only: z11.boolean().optional().describe("Only return public symbols"),
+  include_popularity: z11.boolean().optional().describe("Include callerCount for each symbol (slightly slower)"),
+  limit: z11.coerce.number().int().min(1).max(100).optional().describe("Max symbols to return (max 100)"),
   mode: schemas.navigationMode,
   wait_timeout_ms: schemas.waitTimeoutMs
 };
@@ -7267,7 +7460,7 @@ function createListSymbolsTool(pkgseerService) {
   return {
     name: "list_symbols",
     description: "Browse a dependency's public API or file-level symbols. " + "Accepts package scope (registry + package_name) or repo scope (repo_url + git_ref) via the target parameter. " + "Use scope='exports' for the public API with optional popularity ranking. " + "Use scope='file' with file_path for all symbols in a specific file. " + "Returns symbol refs, names, qualified paths, kinds, and file locations. " + "Use find_symbol(name=<symbol>, include_code=true) to read source for any result.",
-    schema: argsSchema9,
+    schema: argsSchema10,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("list symbols", async () => {
@@ -7302,19 +7495,23 @@ function createListSymbolsTool(pkgseerService) {
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
-        return textResult(JSON.stringify(result.data.listSymbols, null, 2));
+        const data = result.data.listSymbols;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
+        return textResult(JSON.stringify(data, null, 2));
       });
     }
   };
 }
 // src/tools/package-dependencies.ts
-import { z as z11 } from "zod";
-var argsSchema10 = {
+import { z as z12 } from "zod";
+var argsSchema11 = {
   registry: schemas.registry,
   package_name: schemas.packageName.describe("Name of the package to retrieve dependencies for"),
   version: schemas.version,
-  include_transitive: z11.boolean().optional().describe("Whether to include transitive dependency DAG"),
-  max_depth: z11.coerce.number().int().min(1).max(10).optional().describe("Maximum depth for transitive traversal (1-10)")
+  include_transitive: z12.boolean().optional().describe("Whether to include transitive dependency DAG"),
+  max_depth: z12.coerce.number().int().min(1).max(10).optional().describe("Maximum depth for transitive traversal (1-10)")
 };
 function decodeDag(rawDag) {
   if (!rawDag || typeof rawDag !== "object")
@@ -7392,7 +7589,7 @@ function createPackageDependenciesTool(pkgseerService) {
   return {
     name: "package_dependencies",
     description: "Analyze package dependencies. By default returns direct dependencies only. " + "Set include_transitive=true to get the full dependency tree (use max_depth to limit large trees). " + "Returns: dependency names, version constraints, and for transitive deps, a graph with depth levels. " + "Use this to understand complexity before adding a package, or to find nested dependencies.",
-    schema: argsSchema10,
+    schema: argsSchema11,
     annotations: { readOnlyHint: true },
     handler: async ({ registry, package_name, version: version2, include_transitive, max_depth }, _extra) => {
       return withErrorHandling("fetch package dependencies", async () => {
@@ -7431,7 +7628,7 @@ function createPackageDependenciesTool(pkgseerService) {
   };
 }
 // src/tools/package-quality.ts
-var argsSchema11 = {
+var argsSchema12 = {
   registry: schemas.registry,
   package_name: schemas.packageName.describe("Name of the package to analyze"),
   version: schemas.version
@@ -7440,7 +7637,7 @@ function createPackageQualityTool(pkgseerService) {
   return {
     name: "package_quality",
     description: "Evaluate package maintenance health and code quality (available immediately — no indexing required). " + "Use this to assess if a package is well-maintained " + "before adding it as a dependency. Returns: overall score (0-100), category scores (documentation, " + "testing, community, maintenance), and individual rule results with pass/fail status. " + "Useful for comparing quality between alternative packages.",
-    schema: argsSchema11,
+    schema: argsSchema12,
     annotations: { readOnlyHint: true },
     handler: async ({ registry, package_name, version: version2 }, _extra) => {
       return withErrorHandling("fetch package quality", async () => {
@@ -7457,7 +7654,7 @@ function createPackageQualityTool(pkgseerService) {
   };
 }
 // src/tools/package-summary.ts
-var argsSchema12 = {
+var argsSchema13 = {
   registry: schemas.registry,
   package_name: schemas.packageName.describe("Name of the package to retrieve summary for")
 };
@@ -7465,7 +7662,7 @@ function createPackageSummaryTool(pkgseerService) {
   return {
     name: "package_summary",
     description: "Get a comprehensive overview of a package (available immediately — no indexing required). " + "Use this as your first tool when researching a package. " + "Returns: description, latest version, license, repository URL, download stats, " + "active security advisories count, and quickstart/installation instructions. " + "For deeper analysis, follow up with package_quality (maintenance health) or " + "package_vulnerabilities (security details). " + "Use package.repositoryUrl + package.latestVersion as git_ref with fetch_code_context to read source files.",
-    schema: argsSchema12,
+    schema: argsSchema13,
     annotations: { readOnlyHint: true },
     handler: async ({ registry, package_name }, _extra) => {
       return withErrorHandling("fetch package summary", async () => {
@@ -7482,7 +7679,7 @@ function createPackageSummaryTool(pkgseerService) {
   };
 }
 // src/tools/package-vulnerabilities.ts
-var argsSchema13 = {
+var argsSchema14 = {
   registry: schemas.registry,
   package_name: schemas.packageName.describe("Name of the package to inspect for vulnerabilities"),
   version: schemas.version
@@ -7491,7 +7688,7 @@ function createPackageVulnerabilitiesTool(pkgseerService) {
   return {
     name: "package_vulnerabilities",
     description: "Check security vulnerabilities for a package (available immediately — no indexing required). " + "Use this before adding dependencies or when auditing existing ones. " + "Returns: list of CVEs/advisories with severity levels, affected version ranges, fixed versions, " + "and upgrade recommendations. If version is specified, shows only vulnerabilities affecting that version.",
-    schema: argsSchema13,
+    schema: argsSchema14,
     annotations: { readOnlyHint: true },
     handler: async ({ registry, package_name, version: version2 }, _extra) => {
       return withErrorHandling("fetch package vulnerabilities", async () => {
@@ -7508,21 +7705,21 @@ function createPackageVulnerabilitiesTool(pkgseerService) {
   };
 }
 // src/tools/read-file.ts
-import { z as z12 } from "zod";
-var argsSchema14 = {
+import { z as z13 } from "zod";
+var argsSchema15 = {
   target: schemas.codeTarget,
-  file_path: z12.string({
+  file_path: z13.string({
     error: "file_path is required. Get file paths from find_symbol (returns file locations) " + "or list_files (browse file structure)."
   }).min(1).describe("Path to file in repository. Example: src/router/index.js"),
-  start_line: z12.coerce.number().int().positive().optional().describe("Starting line (1-indexed). If omitted, starts from line 1."),
-  end_line: z12.coerce.number().int().positive().optional().describe("Ending line. If omitted, returns to end of file."),
+  start_line: z13.coerce.number().int().positive().optional().describe("Starting line (1-indexed). If omitted, starts from line 1."),
+  end_line: z13.coerce.number().int().positive().optional().describe("Ending line. If omitted, returns to end of file."),
   wait_timeout_ms: schemas.waitTimeoutMs
 };
 function createReadFileTool(pkgseerService) {
   return {
     name: "read_file",
     description: "Read source code from a dependency's repository by file path and line range — " + "use when you have a file path from a stack trace or symbol lookup. " + "Accepts package scope (registry + package_name) or repo scope (repo_url + git_ref) via the target parameter. " + "Returns full file or a specific line range. " + "Prefer find_symbol(include_code=true) for function/class lookup. " + "Use list_files to discover file paths. " + "With repo scope, operates on the full repository. " + "With package scope, scoped to the package subdirectory in monorepos.",
-    schema: argsSchema14,
+    schema: argsSchema15,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("read file", async () => {
@@ -7541,31 +7738,39 @@ function createReadFileTool(pkgseerService) {
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
-        if (!result.data?.fetchCodeContext) {
+        const codeContext = result.data?.fetchCodeContext;
+        if (codeContext) {
+          const indexingError = handleIndexingStatus(codeContext);
+          if (indexingError)
+            return indexingError;
+        }
+        if (!codeContext) {
           return errorResult(`File not found: ${args.file_path}. ` + "Check that the file path and target are correct. " + "Use list_files to discover available files.");
         }
-        return textResult(JSON.stringify(result.data.fetchCodeContext, null, 2));
+        return textResult(JSON.stringify(codeContext, null, 2));
       });
     }
   };
 }
 // src/tools/search.ts
-import { z as z13 } from "zod";
-var packageInputSchema2 = z13.object({
-  registry: schemas.registry,
-  name: z13.string().min(1).describe("Package name"),
-  version: z13.string().optional().describe("Specific version (defaults to latest)")
-});
-var argsSchema15 = {
-  packages: z13.array(packageInputSchema2, {
-    error: 'packages is required. Provide 1-20 packages as [{registry: "npm", name: "express"}]. ' + "Use package_summary to verify a package exists. " + "For project-wide doc search without specifying packages, use search_project_docs instead."
-  }).min(1).max(20).describe('Packages to search (1-20). Format: [{"registry":"npm","name":"express"}]'),
-  query: z13.string({
+import { z as z14 } from "zod";
+var targetInputSchema = z14.object({
+  registry: z14.enum(["npm", "pypi", "hex", "crates", "nuget", "maven", "zig", "vcpkg"]).optional().describe("Package registry (npm, pypi, hex, etc.). Required for package scope."),
+  package_name: z14.string().min(1).optional().describe("Package name. Required for package scope."),
+  version: z14.string().optional().describe("Specific version (defaults to latest). Package scope only."),
+  repo_url: z14.string().optional().describe("Repository URL (GitHub). Required for repo scope. Example: https://github.com/expressjs/express"),
+  git_ref: z14.string().optional().describe("Git ref — tag, branch, or commit. Required for repo scope. Use HEAD for latest.")
+}).describe("Search target: provide registry + package_name (package scope) OR repo_url + git_ref (repo scope).");
+var argsSchema16 = {
+  targets: z14.array(targetInputSchema, {
+    error: 'targets is required. Provide 1-20 targets as [{registry: "npm", package_name: "express"}] ' + 'or [{repo_url: "https://github.com/user/repo", git_ref: "HEAD"}]. ' + "Use package_summary to verify a package exists. " + "For project-wide doc search without specifying targets, use search_project_docs instead."
+  }).min(1).max(20).describe("Targets to search (1-20). Each uses registry + package_name (package scope) or repo_url + git_ref (repo scope)."),
+  query: z14.string({
     error: "query is required. Provide search terms as natural language or keywords, " + "e.g., 'error handling middleware'."
   }).min(1).describe("Search query - natural language or keywords"),
-  mode: z13.enum(["all", "code", "docs"]).optional().describe('Search mode: "all" (default), "code" only, or "docs" only'),
-  limit: z13.coerce.number().int().min(1).max(100).optional().describe("Maximum results (default: 20)"),
-  waitTimeoutMs: z13.coerce.number().int().min(0).max(60000).optional().describe("Max milliseconds to wait for indexing (default: 10000, 0=immediate)")
+  mode: z14.enum(["all", "code", "docs"]).optional().describe('Search mode: "all" (default), "code" only, or "docs" only'),
+  limit: z14.coerce.number().int().min(1).max(100).optional().describe("Maximum results (default: 20)"),
+  wait_timeout_ms: schemas.waitTimeoutMs
 };
 function toSearchMode2(mode) {
   if (!mode)
@@ -7577,6 +7782,47 @@ function toSearchMode2(mode) {
   };
   return map[mode.toLowerCase()];
 }
+function validateAndConvertTargets(targets) {
+  const inputs = [];
+  for (let i = 0;i < targets.length; i++) {
+    const t = targets[i];
+    const hasPackage = t.registry || t.package_name;
+    const hasRepo = t.repo_url || t.git_ref;
+    if (hasPackage && hasRepo) {
+      return {
+        error: `Target ${i + 1}: provide either registry + package_name or repo_url + git_ref, not both.`
+      };
+    }
+    if (!hasPackage && !hasRepo) {
+      return {
+        error: `Target ${i + 1}: provide registry + package_name (package scope) or repo_url + git_ref (repo scope).`
+      };
+    }
+    if (hasPackage) {
+      if (!t.registry || !t.package_name) {
+        return {
+          error: `Target ${i + 1}: both registry and package_name are required for package scope.`
+        };
+      }
+      inputs.push({
+        registry: toGraphQLRegistry(t.registry),
+        name: t.package_name,
+        version: t.version
+      });
+    } else {
+      if (!t.repo_url || !t.git_ref) {
+        return {
+          error: `Target ${i + 1}: both repo_url and git_ref are required for repo scope.`
+        };
+      }
+      inputs.push({
+        repoUrl: t.repo_url,
+        gitRef: t.git_ref
+      });
+    }
+  }
+  return { inputs };
+}
 function formatIndexingWarnings2(indexingStatus) {
   if (!indexingStatus || indexingStatus.length === 0)
     return null;
@@ -7595,7 +7841,7 @@ function formatIndexingWarnings2(indexingStatus) {
   if (warnings.length === 0)
     return null;
   return `
-Note: Some packages are not fully indexed:
+Note: Some targets are not fully indexed:
 ` + warnings.join(`
 `) + `
 Results may be incomplete. Retry later for more complete results.`;
@@ -7603,38 +7849,37 @@ Results may be incomplete. Retry later for more complete results.`;
 function createSearchTool(pkgseerService) {
   return {
     name: "search",
-    description: "Search code and documentation across packages using full-text search. " + "Returns code chunks and doc pages matching your query with relevance scores and snippets. " + "Use mode='code' for code only, mode='docs' for docs only, or mode='all' (default). " + "Provide 1-20 packages. For symbol-level results that feed into symbol_callers/symbol_callees, " + "use search_symbols instead. " + "For full source of code results, use find_symbol(name=<title>, include_code=true). " + "Code results include repoUrl and filePath for use with fetch_code_context. " + "If packages need indexing, waits up to waitTimeoutMs (default 10s) or returns searchRef — use search_status to poll.",
-    schema: argsSchema15,
+    description: "Search code and documentation across packages or repositories using full-text search. " + "Returns code chunks and doc pages matching your query with relevance scores and snippets. " + "Each target can use package scope (registry + package_name) or repo scope (repo_url + git_ref). " + "Use mode='code' for code only, mode='docs' for docs only, or mode='all' (default). " + "Provide 1-20 targets. For symbol-level results that feed into symbol_callers/symbol_callees, " + "use search_symbols instead. " + "For full source of code results, use find_symbol(name=<title>, include_code=true). " + "Code results include repoUrl and filePath for use with fetch_code_context. " + "If targets need indexing, waits up to wait_timeout_ms (default 10s) or returns searchRef — use search_status to poll.",
+    schema: argsSchema16,
     annotations: { readOnlyHint: true },
-    handler: async ({ packages, query, mode, limit, waitTimeoutMs }, _extra) => {
-      return withErrorHandling("search packages", async () => {
+    handler: async ({ targets, query, mode, limit, wait_timeout_ms }, _extra) => {
+      return withErrorHandling("search", async () => {
         const normalizedQuery = query.trim();
         if (normalizedQuery.length === 0) {
           return errorResult("Search query is required.");
         }
-        const graphqlPackages = packages.map((pkg) => ({
-          registry: toGraphQLRegistry(pkg.registry),
-          name: pkg.name,
-          version: pkg.version
-        }));
-        const result = await pkgseerService.combinedSearch(graphqlPackages, normalizedQuery, {
+        const validated = validateAndConvertTargets(targets);
+        if ("error" in validated) {
+          return errorResult(validated.error);
+        }
+        const result = await pkgseerService.combinedSearch(validated.inputs, normalizedQuery, {
           mode: toSearchMode2(mode),
           limit,
-          waitTimeoutMs: waitTimeoutMs ?? DEFAULT_WAIT_TIMEOUT_MS2
+          waitTimeoutMs: wait_timeout_ms ?? DEFAULT_WAIT_TIMEOUT_MS2
         });
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
         const asyncResult = result.data?.combinedSearch;
         if (!asyncResult) {
-          return errorResult("No search results returned. Check package names and registries.");
+          return errorResult("No search results returned. Check target names and registries.");
         }
         if (!asyncResult.completed) {
           const progressInfo = {
             completed: false,
             searchRef: asyncResult.searchRef,
             progress: asyncResult.progress,
-            message: "Search is still indexing. Retry with same query for results, " + "or increase waitTimeoutMs to wait longer."
+            message: "Search is still indexing. Use search_status with the searchRef to poll, " + "or retry with a longer wait_timeout_ms."
           };
           return textResult(JSON.stringify(progressInfo, null, 2));
         }
@@ -7644,7 +7889,7 @@ function createSearchTool(pkgseerService) {
         }
         const entries = searchResult.entries ?? [];
         if (entries.length === 0) {
-          return errorResult(`No results found for "${normalizedQuery}". ` + "Try broader terms or different packages.");
+          return errorResult(`No results found for "${normalizedQuery}". ` + "Try broader terms or different targets.");
         }
         let response = JSON.stringify(searchResult, null, 2);
         const indexingWarning = formatIndexingWarnings2(searchResult.indexingStatus);
@@ -7657,21 +7902,21 @@ function createSearchTool(pkgseerService) {
   };
 }
 // src/tools/search-project-docs.ts
-import { z as z14 } from "zod";
-var argsSchema16 = {
-  project_directory: z14.string().optional().describe("Directory to search for pkgseer.yml configuration. " + "Use this to specify which project's context to use when the MCP server " + "is installed at user level. Defaults to MCP server's working directory."),
-  project: z14.string().optional().describe("Project name to search. Overrides value from pkgseer.yml if provided."),
-  terms: z14.array(z14.string()).optional().describe("Search terms to match. Provide a few key words or phrases that should appear in results."),
-  match_mode: z14.enum(["any", "or", "all", "and"]).optional().describe('How to combine terms: "any" (OR) or "all" (AND).'),
-  include_snippets: z14.boolean().optional().describe("Include content excerpts around matches"),
-  limit: z14.coerce.number().int().min(1).max(100).optional().describe("Maximum number of results to return")
+import { z as z15 } from "zod";
+var argsSchema17 = {
+  project_directory: z15.string().optional().describe("Directory to search for pkgseer.yml configuration. " + "Use this to specify which project's context to use when the MCP server " + "is installed at user level. Defaults to MCP server's working directory."),
+  project: z15.string().optional().describe("Project name to search. Overrides value from pkgseer.yml if provided."),
+  terms: z15.array(z15.string()).optional().describe("Search terms to match. Provide a few key words or phrases that should appear in results."),
+  match_mode: z15.enum(["any", "or", "all", "and"]).optional().describe('How to combine terms: "any" (OR) or "all" (AND).'),
+  include_snippets: z15.boolean().optional().describe("Include content excerpts around matches"),
+  limit: z15.coerce.number().int().min(1).max(100).optional().describe("Maximum number of results to return")
 };
 function createSearchProjectDocsTool(deps) {
   const { pkgseerService, configService, defaultProjectDir } = deps;
   return {
     name: "search_project_docs",
     description: "Search documentation across all dependencies in a PkgSeer project — " + "use when you need to find information but don't know which dependency has it. " + "Requires a pkgseer.yml project config (or pass project name directly). " + "Returns ranked results with snippets from multiple packages. " + "Use project_directory to specify which project's context to use. " + "For single-package doc search, use search(mode='docs') instead.",
-    schema: argsSchema16,
+    schema: argsSchema17,
     annotations: { readOnlyHint: true },
     handler: async ({
       project_directory,
@@ -7720,15 +7965,15 @@ function createSearchProjectDocsTool(deps) {
   };
 }
 // src/tools/search-status.ts
-import { z as z15 } from "zod";
-var argsSchema17 = {
-  searchRef: z15.string().min(1).describe("Search reference from a previous incomplete search")
+import { z as z16 } from "zod";
+var argsSchema18 = {
+  searchRef: z16.string().min(1).describe("Search reference from a previous incomplete search")
 };
 function createSearchStatusTool(pkgseerService) {
   return {
     name: "search_status",
     description: "Check the status of an async search and get results if complete. " + "Use after search returns completed=false with a searchRef. Sessions expire after 1 hour. " + "Returns status (PENDING, INDEXING, SEARCHING, COMPLETED, TIMEOUT, FAILED), " + "progress info (packagesReady/packagesTotal), and results when COMPLETED.",
-    schema: argsSchema17,
+    schema: argsSchema18,
     annotations: { readOnlyHint: true },
     handler: async ({ searchRef }, _extra) => {
       return withErrorHandling("check search status", async () => {
@@ -7770,13 +8015,13 @@ function createSearchStatusTool(pkgseerService) {
   };
 }
 // src/tools/search-symbols.ts
-import { z as z16 } from "zod";
-var argsSchema18 = {
+import { z as z17 } from "zod";
+var argsSchema19 = {
   target: schemas.codeTarget,
-  query: z16.string().max(500).optional().describe("Search query for full-text code search (max 500 chars). Required if keywords not provided."),
-  keywords: z16.array(z16.string()).max(20).optional().describe("Search keywords (max 20). Combined using match_mode. Alternative to query."),
-  match_mode: z16.enum(["or", "and"]).optional().describe("How to combine keywords: or (any match) or and (all must match)"),
-  kind: z16.enum([
+  query: z17.string().max(500).optional().describe("Search query for full-text code search (max 500 chars). Required if keywords not provided."),
+  keywords: z17.array(z17.string()).max(20).optional().describe("Search keywords (max 20). Combined using match_mode. Alternative to query."),
+  match_mode: z17.enum(["or", "and"]).optional().describe("How to combine keywords: or (any match) or and (all must match)"),
+  kind: z17.enum([
     "function",
     "method",
     "class",
@@ -7785,8 +8030,8 @@ var argsSchema18 = {
     "type",
     "doc_section"
   ]).optional().describe("Filter results by code chunk type"),
-  file_path: z16.string().optional().describe("Filter results to files whose path starts with this value (e.g., 'src/' for a directory)"),
-  limit: z16.coerce.number().int().min(1).max(50).optional().describe("Max results to return (max 50)"),
+  file_path: z17.string().optional().describe("Filter results to files whose path starts with this value (e.g., 'src/' for a directory)"),
+  limit: z17.coerce.number().int().min(1).max(50).optional().describe("Max results to return (max 50)"),
   mode: schemas.navigationMode,
   wait_timeout_ms: schemas.waitTimeoutMs
 };
@@ -7794,7 +8039,7 @@ function createSearchSymbolsTool(pkgseerService) {
   return {
     name: "search_symbols",
     description: "Search a dependency's source code by text using the code navigation index — " + "find where error messages, exceptions, or patterns appear across functions, classes, and modules. " + "Accepts package scope (registry + package_name) or repo scope (repo_url + git_ref) via the target parameter. " + "Supports query string or keyword list with match_mode. " + "Use file_path to filter by directory (e.g., 'src/'). " + "Returns symbol-level results that can feed directly into symbol_callers, symbol_callees, or call_path. " + "Follow up with find_symbol(name=<result.name>, include_code=true) for full source. " + "For free-form text search across multiple packages, use search(mode='code') instead.",
-    schema: argsSchema18,
+    schema: argsSchema19,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("search symbols", async () => {
@@ -7819,6 +8064,9 @@ function createSearchSymbolsTool(pkgseerService) {
         if (graphqlError)
           return graphqlError;
         const data = result.data.searchSymbols;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
         const extra = {};
         if (data.results.length === 0 && data.diagnostics?.hint) {
           extra._hint = data.diagnostics.hint;
@@ -7835,13 +8083,13 @@ function createSearchSymbolsTool(pkgseerService) {
   };
 }
 // src/tools/symbol-callees.ts
-import { z as z17 } from "zod";
-var argsSchema19 = {
+import { z as z18 } from "zod";
+var argsSchema20 = {
   symbol: schemas.symbolReference.describe("Symbol to find callees for. Provide symbol_ref, or registry + package_name + symbol_name, or repo_url + git_ref + symbol_name."),
-  max_depth: z17.coerce.number().int().min(1).max(5).optional().describe("BFS traversal depth (1 = direct callees only, 2+ = transitive, max 5)"),
-  limit: z17.coerce.number().int().min(1).max(100).optional().describe("Maximum dependency entries to return"),
-  include_external: z17.boolean().optional().describe("Include calls to symbols in other indexed packages. " + "Default (false) shows only calls within the same package."),
-  include_builtins: z17.boolean().optional().describe("Include calls to built-in/standard library functions (console, Math, etc.)"),
+  max_depth: z18.coerce.number().int().min(1).max(5).optional().describe("BFS traversal depth (1 = direct callees only, 2+ = transitive, max 5)"),
+  limit: z18.coerce.number().int().min(1).max(100).optional().describe("Maximum dependency entries to return"),
+  include_external: z18.boolean().optional().describe("Include calls to symbols in other indexed packages. " + "Default (false) shows only calls within the same package."),
+  include_builtins: z18.boolean().optional().describe("Include calls to built-in/standard library functions (console, Math, etc.)"),
   mode: schemas.navigationMode,
   wait_timeout_ms: schemas.waitTimeoutMs
 };
@@ -7849,7 +8097,7 @@ function createSymbolCalleesTool(pkgseerService) {
   return {
     name: "symbol_callees",
     description: "Trace what a function calls internally — " + "understand dependency behavior by following its execution path. " + "Returns direct callees at max_depth=1, or transitive call chains at higher depths. " + "Includes callee names, qualified paths, file locations, call lines, and external package references. " + "Supports package scope (registry + package_name) or repo scope (repo_url + git_ref). " + "Get symbol_ref from find_symbol or list_symbols. See symbol_callers for the reverse.",
-    schema: argsSchema19,
+    schema: argsSchema20,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("find symbol callees", async () => {
@@ -7868,18 +8116,22 @@ function createSymbolCalleesTool(pkgseerService) {
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
-        return textResult(JSON.stringify(result.data.symbolDependencies, null, 2));
+        const data = result.data.symbolDependencies;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
+        return textResult(JSON.stringify(data, null, 2));
       });
     }
   };
 }
 // src/tools/symbol-callers.ts
-import { z as z18 } from "zod";
-var argsSchema20 = {
+import { z as z19 } from "zod";
+var argsSchema21 = {
   symbol: schemas.symbolReference.describe("Symbol to find callers for. Provide symbol_ref, or registry + package_name + symbol_name, or repo_url + git_ref + symbol_name."),
-  same_package_only: z18.boolean().optional().describe("Only return callers from the same package. " + "Default (false) includes callers from other indexed packages."),
-  max_depth: z18.coerce.number().int().min(1).max(5).optional().describe("BFS traversal depth (1 = direct callers only, 2+ = transitive, max 5)"),
-  limit: z18.coerce.number().int().min(1).max(100).optional().describe("Maximum entries to return"),
+  same_package_only: z19.boolean().optional().describe("Only return callers from the same package. " + "Default (false) includes callers from other indexed packages."),
+  max_depth: z19.coerce.number().int().min(1).max(5).optional().describe("BFS traversal depth (1 = direct callers only, 2+ = transitive, max 5)"),
+  limit: z19.coerce.number().int().min(1).max(100).optional().describe("Maximum entries to return"),
   mode: schemas.navigationMode,
   wait_timeout_ms: schemas.waitTimeoutMs
 };
@@ -7887,7 +8139,7 @@ function createSymbolCallersTool(pkgseerService) {
   return {
     name: "symbol_callers",
     description: "Trace what calls a function in a dependency's source code — " + "find entry points or debug why behavior triggers. " + "Returns callers with file locations and call line numbers. " + "Supports package scope (registry + package_name) or repo scope (repo_url + git_ref). " + "Use same_package_only for within-package callers only. " + "Get symbol_ref from find_symbol or list_symbols. See symbol_callees for the reverse. " + "Use find_symbol(include_code=true) on any caller to read its source.",
-    schema: argsSchema20,
+    schema: argsSchema21,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("find symbol callers", async () => {
@@ -7905,32 +8157,36 @@ function createSymbolCallersTool(pkgseerService) {
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
-        return textResult(JSON.stringify(result.data.symbolDependents, null, 2));
+        const data = result.data.symbolDependents;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
+        return textResult(JSON.stringify(data, null, 2));
       });
     }
   };
 }
 // src/tools/trigger-indexing.ts
-import { z as z19 } from "zod";
-var packageInputSchema3 = z19.object({
+import { z as z20 } from "zod";
+var packageInputSchema2 = z20.object({
   registry: schemas.registry,
-  name: z19.string().max(255).describe("Package name"),
-  version: z19.string().max(100).optional().describe("Specific version to index")
+  name: z20.string().max(255).describe("Package name"),
+  version: z20.string().max(100).optional().describe("Specific version to index")
 });
-var repositoryInputSchema = z19.object({
-  url: z19.string().max(2000).describe("GitHub repository URL"),
-  ref: z19.string().max(200).optional().describe("Git ref to index (tag, branch, commit). Defaults to HEAD"),
-  discover_packages: z19.boolean().optional().describe("If true, discover packages published from this repo and trigger their metadata fetch")
+var repositoryInputSchema = z20.object({
+  url: z20.string().max(2000).describe("GitHub repository URL"),
+  ref: z20.string().max(200).optional().describe("Git ref to index (tag, branch, commit). Defaults to HEAD"),
+  discover_packages: z20.boolean().optional().describe("If true, discover packages published from this repo and trigger their metadata fetch")
 });
-var argsSchema21 = {
-  packages: z19.array(packageInputSchema3).max(100).optional().describe("Package versions to index (max 100)"),
-  repositories: z19.array(repositoryInputSchema).max(50).optional().describe("Repository URLs to index (max 50)")
+var argsSchema22 = {
+  packages: z20.array(packageInputSchema2).max(100).optional().describe("Package versions to index (max 100)"),
+  repositories: z20.array(repositoryInputSchema).max(50).optional().describe("Repository URLs to index (max 50)")
 };
 function createTriggerIndexingTool(pkgseerService) {
   return {
     name: "trigger_indexing",
     description: "Pre-warm PkgSeer indexes by triggering indexing for packages and/or repositories. " + "Fire-and-forget: triggers jobs and returns immediately with accepted/skipped counts. " + "Use before search or doc requests to ensure packages are indexed. " + "Code tools auto-wait via wait_timeout_ms on subsequent calls. Most packages index within 10-30s. " + "Rate limited to 10 requests per minute.",
-    schema: argsSchema21,
+    schema: argsSchema22,
     annotations: { readOnlyHint: false, idempotentHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("trigger indexing", async () => {
@@ -7968,13 +8224,13 @@ function createTriggerIndexingTool(pkgseerService) {
   };
 }
 // src/tools/version-diff.ts
-import { z as z20 } from "zod";
-var argsSchema22 = {
+import { z as z21 } from "zod";
+var argsSchema23 = {
   target: schemas.codeTarget,
-  from_version: z20.string().max(100).describe("Source version (git ref, e.g., 'v4.18.2')"),
-  to_version: z20.string().max(100).describe("Target version (git ref, e.g., 'v5.0.0')"),
-  include_private: z20.boolean().optional().describe("Include private/non-exported symbols in the diff"),
-  kind: z20.enum([
+  from_version: z21.string().max(100).describe("Source version (git ref, e.g., 'v4.18.2')"),
+  to_version: z21.string().max(100).describe("Target version (git ref, e.g., 'v5.0.0')"),
+  include_private: z21.boolean().optional().describe("Include private/non-exported symbols in the diff"),
+  kind: z21.enum([
     "function",
     "method",
     "class",
@@ -7983,14 +8239,14 @@ var argsSchema22 = {
     "type",
     "doc_section"
   ]).optional().describe("Filter by symbol kind"),
-  limit: z20.coerce.number().int().min(1).max(500).optional().describe("Max changes to return (max 500). Summary always reflects full counts."),
+  limit: z21.coerce.number().int().min(1).max(500).optional().describe("Max changes to return (max 500). Summary always reflects full counts."),
   wait_timeout_ms: schemas.waitTimeoutMs
 };
 function createVersionDiffTool(pkgseerService) {
   return {
     name: "version_diff",
     description: "Compare two versions of a dependency to understand what changed — " + "use when debugging issues after upgrades or planning migrations. " + "Accepts package scope (registry + package_name) or repo scope (repo_url + git_ref) via the target parameter. " + "With repo scope, from_version and to_version are literal git refs (tags, branches, commits) — " + "the backend does not normalize them. Use target.git_ref=HEAD to identify the repository. " + "Detects added, removed, moved, and modified symbols with severity " + "(breaking, behavior_change, non_breaking, internal). " + "Returns summary counts and per-symbol changes with file locations.",
-    schema: argsSchema22,
+    schema: argsSchema23,
     annotations: { readOnlyHint: true },
     handler: async (args, _extra) => {
       return withErrorHandling("version diff", async () => {
@@ -8009,7 +8265,11 @@ function createVersionDiffTool(pkgseerService) {
         const graphqlError = handleGraphQLErrors(result.errors);
         if (graphqlError)
           return graphqlError;
-        return textResult(JSON.stringify(result.data.versionDiff, null, 2));
+        const data = result.data.versionDiff;
+        const indexingError = handleIndexingStatus(data);
+        if (indexingError)
+          return indexingError;
+        return textResult(JSON.stringify(data, null, 2));
       });
     }
   };
@@ -8049,7 +8309,7 @@ Data availability — tools are grouped by what backend data they need:
 3. Code navigation (requires code repo indexing, dual addressing via target):
    find_symbol, list_symbols, search_symbols, symbol_callers, symbol_callees, call_path,
    list_imports, version_diff, list_files, grep_file, read_file, search(mode='code')
-   These wait up to wait_timeout_ms (default 10s) for indexing. If indexing takes longer, you'll get a "being indexed" response — retry the same call. Most packages index within 10-30 seconds.
+   These wait up to wait_timeout_ms (default 10s) for indexing. If indexing takes longer, the response includes an indexingRef — use indexing_status to poll progress, then retry the original query when status is INDEXED.
 
 Symbol reference tools (symbol_callers, symbol_callees, call_path) accept a symbol object with either:
 - symbol_ref from a previous find_symbol/search_symbols result (preferred, fastest)
@@ -8062,7 +8322,7 @@ Choosing a code search tool:
 - search(mode='code'): multi-package, full-text → code chunks with snippets
 - grep_file: single file, pattern match → when you know the file path
 
-Utility: trigger_indexing (pre-warm indexes), search_status (poll async search).
+Utility: trigger_indexing (pre-warm indexes), search_status (poll async search), indexing_status (poll navigation indexing).
 
 Quick start: find_symbol(target={registry:"npm", package_name:"<pkg>"}, name="<function>", include_code=true) often answers the question in one call.
 
@@ -8071,7 +8331,7 @@ Common workflows (pass symbolRef between tools for chaining):
 - Trace calls: find_symbol → symbol_callees(symbol={symbol_ref: <symbolRef>})
 - Find callers: find_symbol → symbol_callers(symbol={symbol_ref: <symbolRef>})
 - Read file: read_file(target={registry, package_name}, file_path=<path>) or read_file(target={repo_url, git_ref}, file_path=<path>)
-- Search code: search_symbols (single pkg, feeds callers/callees) or search(mode='code', packages=[...]) (multi-pkg)
+- Search code: search_symbols (single pkg, feeds callers/callees) or search(mode='code', targets=[...]) (multi-target)
 - Browse docs: list_package_docs → fetch_package_doc(page_id)`;
 var TOOL_FACTORIES = {
   package_summary: ({ pkgseerService }) => createPackageSummaryTool(pkgseerService),
@@ -8097,6 +8357,7 @@ var TOOL_FACTORIES = {
   list_imports: ({ pkgseerService }) => createListImportsTool(pkgseerService),
   call_path: ({ pkgseerService }) => createCallPathTool(pkgseerService),
   trigger_indexing: ({ pkgseerService }) => createTriggerIndexingTool(pkgseerService),
+  indexing_status: ({ pkgseerService }) => createIndexingStatusTool(pkgseerService),
   list_files: ({ pkgseerService }) => createListFilesTool(pkgseerService),
   grep_file: ({ pkgseerService }) => createGrepFileTool(pkgseerService),
   version_diff: ({ pkgseerService }) => createVersionDiffTool(pkgseerService)
@@ -8120,6 +8381,7 @@ var PUBLIC_READ_TOOLS = [
   "list_imports",
   "call_path",
   "trigger_indexing",
+  "indexing_status",
   "list_files",
   "grep_file",
   "version_diff"
@@ -8188,19 +8450,20 @@ function showMcpSetupInstructions(deps) {
   console.log("Alternative: Use CLI directly (no MCP setup needed)");
   console.log(`  ${highlight("pkgseer pkg info <package>", useColors)}`);
 }
-function registerMcpCommand(program) {
-  const mcpCommand = program.command("mcp").summary("Show setup instructions or start MCP server").description(`Start the Model Context Protocol (MCP) server using STDIO transport.
+var MCP_COMMAND_DESCRIPTION = `Start the Model Context Protocol (MCP) server using STDIO transport.
 
 When run interactively (TTY), shows setup instructions.
 When run via stdio (non-TTY), starts the MCP server.
 
-Available tools (22):
+Available tools (23):
   Navigate source: find_symbol, list_symbols, search_symbols, symbol_callers, symbol_callees, call_path
   Browse files: list_files, grep_file, read_file
   Search: search, search_project_docs
   Docs: list_package_docs, fetch_package_doc
   Evaluate: package_summary, package_quality, package_vulnerabilities, compare_packages, package_dependencies, version_diff
-  Utility: trigger_indexing, search_status, list_imports`).action(async () => {
+  Utility: trigger_indexing, indexing_status, search_status, list_imports`;
+function registerMcpCommand(program) {
+  const mcpCommand = program.command("mcp").summary("Show setup instructions or start MCP server").description(MCP_COMMAND_DESCRIPTION).action(async () => {
     const deps = await createContainer();
     if (process.stdout.isTTY && process.stdin.isTTY) {
       showMcpSetupInstructions(deps);

package/dist/index.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./shared/chunk-kh5enjt9.js";
+} from "./shared/chunk-a0vv3x03.js";
 export {
   version
 };

package/dist/shared/{chunk-kh5enjt9.js → chunk-a0vv3x03.js}

@@ -1,4 +1,4 @@
 // package.json
-var version = "0.5.0";
+var version = "0.5.2";
 
 export { version };

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@pkgseer/cli",
   "description": "CLI companion for PkgSeer - package intelligence for developers and AI assistants",
-  "version": "0.5.0",
+  "version": "0.5.2",
   "type": "module",
   "files": [
     "dist",