token-goat 2.9.15 → 2.9.16

package/dist/{token-goat-chunk-ASYEPR3S.mjs → token-goat-chunk-2IEIBVVD.mjs}

@@ -6,12 +6,13 @@ import {
   collectElements,
   collectParagraphTexts,
   decodeZipEntry,
+  inlineMathRuns,
   ooxmlPartBudget,
   ooxmlWorkDeadline,
   parseOoxmlPart,
   readOoxmlZip,
   sortNumberedParts
-} from "./token-goat-chunk-MZDIJJ3R.mjs";
+} from "./token-goat-chunk-MA5BZ2KI.mjs";
 import {
   compileGuardedRegex
 } from "./token-goat-chunk-GMOUBOX4.mjs";
@@ -107,16 +108,19 @@ async function notesPathFor(entries, slidePath, budget) {
   }
   return null;
 }
+function inlineSlideMath(xml) {
+  return inlineMathRuns(xml, '<a:r><a:t xml:space="preserve">', "</a:t></a:r>").replace(/<a14:m(?:\s[^>]*)?>/g, "").replace(/<\/a14:m>/g, "");
+}
 async function parseSlide(entries, path, budget) {
   const xml = decodeZipEntry(entries, path, budget);
   if (xml === null) throw new Error(`missing part: ${path}`);
-  return parseOoxmlPart(xml);
+  return parseOoxmlPart(inlineSlideMath(xml));
 }
 async function notesTextFor(entries, notesPath, budget) {
   if (notesPath === null) return "";
   const xml = decodeZipEntry(entries, notesPath, budget);
   if (xml === null) return "";
-  const parsed = await parseOoxmlPart(xml);
+  const parsed = await parseOoxmlPart(inlineSlideMath(xml));
   const shapes = collectElements(parsed, "p:sp");
   const bodyShape = shapes.find((s) => shapePlaceholderType(s) === "body");
   return bodyShape !== void 0 ? shapeText(bodyShape) : flatSlideText(parsed);

package/dist/{token-goat-chunk-LCZBPOIN.mjs → token-goat-chunk-2PCFAQAS.mjs}

@@ -1,5 +1,11 @@
 import { createRequire as __cjsRequire } from 'node:module';
 const require = __cjsRequire(import.meta.url);
+import {
+  isOcrEngineAvailable,
+  isTextHeavy,
+  ocrImage,
+  ocrIntegrityFailed
+} from "./token-goat-chunk-EJCY6KHO.mjs";
 import {
   formatSqliteQueryTable,
   formatSqliteSchema,
@@ -13,8 +19,10 @@ import {
   NOTEBOOK_CELL_LINES_SUFFIX,
   SKIP_DIRS,
   canShrinkFormat,
+  capJsonRows,
   emptyIndexMessage,
   enqueueDirtyPathSafe,
+  estimateTokens,
   fenceUntrusted,
   formatSymbolLocation,
   getEmbeddingCoverage,
@@ -30,29 +38,35 @@ import {
   scanAndRecord,
   searchEvidenceSemantically,
   shrinkImage,
+  trimToBudget,
   urlPolicyDenialReason,
   virtualIndexedScopeNote,
   walkProject
-} from "./token-goat-chunk-BL5LNGBG.mjs";
+} from "./token-goat-chunk-XOHTFRDH.mjs";
 import {
-  capJsonRows,
-  estimateTokens,
-  trimToBudget
-} from "./token-goat-chunk-YQ7WI2CO.mjs";
+  colorStdout,
+  isBlobStale,
+  loadBlob,
+  recordStat,
+  redactSecrets,
+  savedTokensFromBytes,
+  storeBlob,
+  stripAnsi
+} from "./token-goat-chunk-DMQ32ZSR.mjs";
 import {
   extractPdfMeta,
   extractPdfOutline,
   extractPdfText,
   locatePdfPages,
   readPdfFileWithinBounds
-} from "./token-goat-chunk-NEI4NC54.mjs";
+} from "./token-goat-chunk-LKSXAMJB.mjs";
 import {
   formatCsvProfile,
   formatCsvTable,
   parseWhereSpecs,
   profileCsv,
   queryCsv
-} from "./token-goat-chunk-YKG35VHC.mjs";
+} from "./token-goat-chunk-GIMGT34T.mjs";
 import {
   MAX_ZIP_INPUT_BYTES,
   MAX_ZIP_OUTPUT_BYTES,
@@ -87,7 +101,7 @@ import {
   extractSolidity,
   extractThrift,
   stripLeadingAttributes
-} from "./token-goat-chunk-XEPXYDPI.mjs";
+} from "./token-goat-chunk-YPS64ACE.mjs";
 import {
   MAX_OVER_FETCH,
   OVER_FETCH_FACTOR,
@@ -100,7 +114,7 @@ import {
   mergeNearbyHits,
   readSection,
   searchSemantic
-} from "./token-goat-chunk-NDRP4KJQ.mjs";
+} from "./token-goat-chunk-BFNTLGVA.mjs";
 import {
   DEFAULT_QUERY_LIMIT,
   countRefs,
@@ -113,23 +127,7 @@ import {
   queryRefsByContext,
   querySymbols,
   searchSymbolsFts
-} from "./token-goat-chunk-2X2EBBC6.mjs";
-import {
-  isOcrEngineAvailable,
-  isTextHeavy,
-  ocrImage,
-  ocrIntegrityFailed
-} from "./token-goat-chunk-SFAS46RE.mjs";
-import {
-  colorStdout,
-  isBlobStale,
-  loadBlob,
-  recordStat,
-  redactSecrets,
-  savedTokensFromBytes,
-  storeBlob,
-  stripAnsi
-} from "./token-goat-chunk-IVUQLQWN.mjs";
+} from "./token-goat-chunk-63QWJ6UM.mjs";
 import {
   FILENAME_LANGUAGE,
   TREE_SITTER_LANGUAGES,
@@ -148,7 +146,7 @@ import {
   partialRefsReason,
   redactIfDotenv,
   unsupportedLanguageName
-} from "./token-goat-chunk-K7F2BFIK.mjs";
+} from "./token-goat-chunk-R3X5TCPB.mjs";
 import {
   fileIsAbsent,
   findProject,
@@ -158,7 +156,7 @@ import {
   loadConfig,
   resolveProjectRoot,
   shortFingerprint
-} from "./token-goat-chunk-S4XRY446.mjs";
+} from "./token-goat-chunk-H3DXI6VD.mjs";
 import {
   registerReset
 } from "./token-goat-chunk-EEIDFMEM.mjs";
@@ -190,7 +188,7 @@ import {
   supportRequestLine,
   windowsCmdQuoteArg,
   withExtension
-} from "./token-goat-chunk-PM76YS22.mjs";
+} from "./token-goat-chunk-3H6FQT62.mjs";
 import {
   UNTRUSTED_FILE_TAG,
   UNTRUSTED_GITHUB_TAG,
@@ -467,6 +465,7 @@ function queryJson(data, spec) {
 // src/read_spec.ts
 init_define_import_meta_env();
 import * as fs13 from "node:fs";
+import * as path13 from "node:path";
 
 // src/read_commands.ts
 init_define_import_meta_env();
@@ -1593,12 +1592,12 @@ function runScope(opts) {
     emitErr(`Invalid line number: ${lineStr}`);
     return 1;
   }
-  const confined = fileConfinementRefusal("This file", file, void 0);
+  const confined = fileConfinementRefusal("This file", file, opts.projectRoot);
   if (confined !== null) {
     emitErr(confined);
     return 1;
   }
-  const filePath = resolveIndexPath(file);
+  const filePath = resolveIndexPath(file, opts.projectRoot ?? process.cwd());
   const enclosing = querySymbols({ filePath, enclosingLine: line, limit: ALL_SYMBOLS_IN_FILE_LIMIT }).sort((a, b) => b.lineStart - a.lineStart || a.lineEnd - b.lineEnd || a.name.localeCompare(b.name, "en"));
   if (enclosing.length === 0) {
     if (querySymbols({ filePath, limit: 1 }).length === 0) {
@@ -1643,7 +1642,7 @@ function buildImportGraph(cwd) {
   const files = getTrackedFiles(cwd);
   const filesByFoldedPath = /* @__PURE__ */ new Map();
   for (const f of files) filesByFoldedPath.set(foldPath(f), f);
-  const resolve7 = (fromFile, spec) => {
+  const resolve8 = (fromFile, spec) => {
     if (!spec.startsWith(".")) return null;
     const dir = path3.dirname(fromFile);
     const strippedSpec = spec.replace(/\.(m?js|cjs)$/, "");
@@ -1670,7 +1669,7 @@ function buildImportGraph(cwd) {
     }
     const internal = [];
     for (const spec of extractImports(text, importsExtensionFor(file))) {
-      const resolved = resolve7(file, spec);
+      const resolved = resolve8(file, spec);
       if (resolved === null) continue;
       internal.push(resolved);
       let importers = importedBy.get(resolved);
@@ -1682,7 +1681,7 @@ function buildImportGraph(cwd) {
     }
     graph.set(file, internal);
   }
-  return { files, graph, importedBy, resolve: resolve7 };
+  return { files, graph, importedBy, resolve: resolve8 };
 }
 
 // src/modules.ts
@@ -2106,7 +2105,7 @@ function runArch(opts) {
   }
   const cwd = opts.cwd ?? process.cwd();
   const top = opts.top ?? 10;
-  const { files, graph, importedBy, resolve: resolve7 } = buildImportGraph(cwd);
+  const { files, graph, importedBy, resolve: resolve8 } = buildImportGraph(cwd);
   if (files.length === 0 && opts.json !== true) {
     emit2(`no tracked files found under '${toDisplayPath(getDisplayRoot(cwd), cwd)}' (is it a git repo?). Nothing to analyse.`);
     return 0;
@@ -2118,7 +2117,7 @@ function runArch(opts) {
   const entryPointsTotal = allEntryPoints.length;
   const entryPoints = allEntryPoints.slice(0, top);
   const { cycles, truncated: cyclesTruncated } = findCyclesCapped(graph);
-  const moduleResult = opts.modules === true ? detectModules({ files, graph, importedBy, resolve: resolve7 }, cwd, top) : null;
+  const moduleResult = opts.modules === true ? detectModules({ files, graph, importedBy, resolve: resolve8 }, cwd, top) : null;
   if (opts.json === true) {
     const modulePayload = moduleResult === null ? {} : { modules: moduleResult.modules, modulesTotal: moduleResult.modulesTotal, modulesTruncated: moduleResult.modules.length < moduleResult.modulesTotal, modularity: moduleResult.modularity, isolatedCount: moduleResult.isolatedCount, crossImports: moduleResult.crossImports, crossImportsTotal: moduleResult.crossImportsTotal, crossImportsTruncated: moduleResult.crossImports.length < moduleResult.crossImportsTotal, noImportEdges: moduleResult.noEdges };
     emit2(displaySafeJson({ hubs, hubsTotal, hubsTruncated: hubs.length < hubsTotal, entryPoints, entryPointsTotal, entryPointsTruncated: entryPoints.length < entryPointsTotal, cycles, ...cyclesTruncated ? { cyclesTruncated: true } : {}, ...modulePayload }));
@@ -2978,7 +2977,7 @@ async function captureOnce(url, ctx) {
       })();
     });
     try {
-      await page.goto(url, { waitUntil: "networkidle2", timeout: 3e4 });
+      await page.goto(url, { waitUntil: "networkidle2", timeout: 6e4 });
     } catch (err) {
       if (hop.url !== null) return { redirectTo: hop.url };
       if (navRefusal.reason !== null) throw new Error(navRefusal.reason, { cause: err });
@@ -8263,7 +8262,7 @@ function filteredToEmptyNotice(preFilterCount, minLines, grep) {
 }
 function prepareSymbolListing(file, opts) {
   const resolved = resolveIndexPath(file, opts.projectRoot ?? process.cwd());
-  const confined = confinementRefusal("This file", resolved, confinedProjectRoot());
+  const confined = confinementRefusal("This file", resolved, confinedProjectRoot(opts.projectRoot));
   if (confined !== null) return { kind: "confined", text: confined };
   if (opts.forceRefresh === true) {
     indexFileSyncPinned(resolved, globalDbPath());
@@ -8481,6 +8480,8 @@ ${emptyIndexMessage(rootDir2)}`, code: 1 };
       truncated,
       ...hiddenByExcludeTests > 0 ? { hiddenByExcludeTests } : {},
       ...hiddenByGrep > 0 ? { hiddenByGrep } : {},
+      // Mirrors runRead's json branch: emitting the row verbatim would hand a JSON consumer a deleted file's stale body with no signal it is no longer live.
+      ...fileIsGone(match.filePath) ? { deleted: true } : {},
       section
     };
     const jsonText = displaySafeJson(result);
@@ -8496,6 +8497,7 @@ ${emptyIndexMessage(rootDir2)}`, code: 1 };
     body,
     ""
   ];
+  const warning = staleWarning(match.filePath);
   const hiddenNote = excludeTests && hiddenByExcludeTests > 0 ? ` (${excludeTestsHiddenNote(hiddenByExcludeTests)})` : "";
   if (callers.length === 0 && matchesGrep !== void 0 && preGrepCount > 0) {
     lines.push(`Callers (0): ${grepFilteredToEmptyNotice(preGrepCount, opts.grep ?? "", "caller", "callers").trim()}`);
@@ -8515,7 +8517,7 @@ ${emptyIndexMessage(rootDir2)}`, code: 1 };
     lines.push("");
     lines.push(`Section: ${section.heading} (lines ${section.lineStart}-${section.lineEnd})`);
   }
-  const text = guardText(trimBlankLines(lines).join("\n"), "symbol");
+  const text = guardText(warning + trimBlankLines(lines).join("\n"), "symbol");
   if (opts.suppressStat !== true) recordReadStat("brief_view", fullSourceBytes, text, opts.spec);
   return { text, code: 0 };
 }
@@ -10723,10 +10725,11 @@ function runSymbol(opts) {
   }
   const matchesGrep = opts.grep !== void 0 ? compileGrepMatcher(opts.grep) : void 0;
   const excludeTests = opts.excludeTests === true;
-  const confinedRoot = confinedProjectRoot();
-  if (confinedRoot !== null) {
+  const baseConfined = confinedProjectRoot();
+  const confinedRoot = opts.projectRoot !== void 0 && baseConfined !== null && isProjectRootAllowed(opts.projectRoot, baseConfined) ? confinedProjectRoot(opts.projectRoot) ?? baseConfined : baseConfined;
+  if (baseConfined !== null) {
     const requested = opts.projectRoot;
-    const projectDenial = requested === void 0 ? null : confinementRefusal("--project", requested, confinedRoot);
+    const projectDenial = requested === void 0 || confinedRoot !== baseConfined ? null : confinementRefusal("--project", requested, baseConfined);
     if (projectDenial !== null) return { text: projectDenial, code: 1 };
     if (opts.file !== void 0) {
       const fileDenial = confinementRefusal("--file", resolveIndexPath(opts.file, requested ?? process.cwd()), confinedRoot);
@@ -11179,9 +11182,11 @@ function runRefs(opts) {
     emitErr4(`--top must be a positive number, got: ${opts.top}`);
     return 1;
   }
-  const confinedRoot = confinedProjectRoot();
-  if (confinedRoot !== null) {
-    const projectDenial = opts.projectRoot === void 0 ? null : confinementRefusal("--project", opts.projectRoot, confinedRoot);
+  const baseConfined = confinedProjectRoot();
+  const confinedRoot = opts.projectRoot !== void 0 && baseConfined !== null && isProjectRootAllowed(opts.projectRoot, baseConfined) ? confinedProjectRoot(opts.projectRoot) ?? baseConfined : baseConfined;
+  if (baseConfined !== null) {
+    const requested = opts.projectRoot;
+    const projectDenial = requested === void 0 || confinedRoot !== baseConfined ? null : confinementRefusal("--project", requested, baseConfined);
     if (projectDenial !== null) {
       emitErr4(projectDenial);
       return 1;
@@ -11835,6 +11840,7 @@ async function runSemantic(query, opts) {
   mergedHits.forEach((h, denseRank) => {
     const enclosing = resolveEnclosingSymbol(h.filePath, h.startLine);
     const key = enclosing !== null ? `${h.filePath}::${enclosing.name}@${enclosing.lineStart}` : `${h.filePath}::L${h.startLine}`;
+    if (fused.has(key)) return;
     fused.set(key, {
       filePath: h.filePath,
       startLine: h.startLine,
@@ -12164,15 +12170,24 @@ function formatAmbiguity(symbol, file, candidates, explicitRoot, commandName = "
   }
   return lines.join("\n");
 }
-function confinedProjectRoot() {
-  return loadConfig().indexing.cross_project_symbols ? null : resolveProjectRoot();
+function confinedProjectRoot(explicitRoot) {
+  if (loadConfig().indexing.cross_project_symbols) return null;
+  return resolveProjectRoot(explicitRoot !== void 0 && explicitRoot.trim().length > 0 ? { project: explicitRoot } : {});
+}
+function isProjectRootAllowed(candidateRoot, baseConfinedRoot) {
+  if (isInsideRoot(candidateRoot, baseConfinedRoot)) return true;
+  const allowedRoots = loadConfig().mcp.allowed_roots;
+  if (allowedRoots.length > 0 && allowedRoots.some((allowed) => isInsideRoot(candidateRoot, path13.resolve(allowed)))) {
+    return true;
+  }
+  return false;
 }
 function confinementRefusal(label, resolved, root) {
   if (root === null || isInsideRoot(resolved, root)) return null;
   return `${label} is outside this project root, and indexing.cross_project_symbols = false confines symbol lookups to it: ${toDisplayPath(root, resolved)}`;
 }
 function fileConfinementRefusal(label, file, projectRoot) {
-  const root = confinedProjectRoot();
+  const root = confinedProjectRoot(projectRoot);
   if (root === null) return null;
   return confinementRefusal(label, resolveIndexPath(file, projectRoot ?? process.cwd()), root);
 }
@@ -12183,7 +12198,7 @@ function resolveSymbolSpec(spec, forceRefresh, projectRoot) {
   const symbol = anchorMatch !== null ? anchorMatch[1] : rawSymbol;
   const lineAnchor = anchorMatch !== null ? parseInt(anchorMatch[2], 10) : void 0;
   const resolved = resolveIndexPath(file, projectRoot ?? process.cwd());
-  const confined = confinementRefusal("This file", resolved, confinedProjectRoot());
+  const confined = confinementRefusal("This file", resolved, confinedProjectRoot(projectRoot));
   if (confined !== null) return { kind: "confined", message: confined };
   if (forceRefresh === true) {
     indexFileSyncPinned(resolved, globalDbPath());
@@ -12290,7 +12305,7 @@ function resolveSymbolSpecOrEmitError(commandName, spec, projectRoot) {
 // src/content_store.ts
 init_define_import_meta_env();
 import { deflateRawSync } from "node:zlib";
-import * as path13 from "node:path";
+import * as path14 from "node:path";
 var CONTENT_MAX_INPUT_CHARS = 512 * 1024;
 var CONTENT_MAX_ITEMS = 256;
 var CONTENT_MAX_BYTES = 32 * 1024 * 1024;
@@ -12313,7 +12328,7 @@ function contentId(text) {
   return `tg_${shortFingerprint(text)}`;
 }
 function normalizeProjectRoot(projectRoot) {
-  const candidate = path13.resolve(projectRoot ?? process.cwd());
+  const candidate = path14.resolve(projectRoot ?? process.cwd());
   return findProject(candidate)?.root ?? candidate;
 }
 function handoffId(name, projectRoot) {

package/dist/{token-goat-chunk-PM76YS22.mjs → token-goat-chunk-3H6FQT62.mjs}

@@ -21,7 +21,7 @@ init_define_import_meta_env();
 import { createRequire } from "node:module";
 function resolveVersion() {
   if (true) {
-    return "2.9.15";
+    return "2.9.16";
   }
   const require2 = createRequire(import.meta.url);
   const pkg = require2("../package.json");

package/dist/{token-goat-chunk-C5JIO6HK.mjs → token-goat-chunk-4DC6DDIB.mjs}

@@ -20,17 +20,17 @@ import {
   setOcrTimeoutForTesting,
   setTesseractEntryForTesting,
   verifyOcrLangCache
-} from "./token-goat-chunk-SFAS46RE.mjs";
-import "./token-goat-chunk-IVUQLQWN.mjs";
-import "./token-goat-chunk-K7F2BFIK.mjs";
+} from "./token-goat-chunk-EJCY6KHO.mjs";
+import "./token-goat-chunk-DMQ32ZSR.mjs";
+import "./token-goat-chunk-R3X5TCPB.mjs";
 import {
   DEFAULT_OCR_LANG,
   isSupportedOcrLang,
   resolveOcrLangs
-} from "./token-goat-chunk-S4XRY446.mjs";
+} from "./token-goat-chunk-H3DXI6VD.mjs";
 import "./token-goat-chunk-EEIDFMEM.mjs";
 import "./token-goat-chunk-OSUFN2FV.mjs";
-import "./token-goat-chunk-PM76YS22.mjs";
+import "./token-goat-chunk-3H6FQT62.mjs";
 import "./token-goat-chunk-ERTXEKB6.mjs";
 import "./token-goat-chunk-GMOUBOX4.mjs";
 import "./token-goat-chunk-A37V4PBF.mjs";