token-goat 2.6.33 → 2.6.34

package/dist/{token-goat-hook-chunk-UWV4MTYI.mjs → token-goat-hook-chunk-6QTWMSRO.mjs}

@@ -10,15 +10,20 @@ import {
   atomicWriteText,
   backupFile,
   buildLineIndex,
+  countContentLines,
   countNoun,
   dataDir,
+  decodeSource,
   detectHarness,
   detectLanguage,
+  displaySafePath,
+  displaySafeText,
   ensureDirSync,
   escapeRegExp,
   extractEnv,
   extractErrorMessage,
   extractIni,
+  fileIsAbsent,
   findHtmlHeadingMatches,
   findMatchingBraceEndLine,
   findProject,
@@ -82,7 +87,7 @@ import {
   withFileLock,
   writeIfDifferent,
   writeJsonSettings
-} from "./token-goat-hook-chunk-E6AIPKNF.mjs";
+} from "./token-goat-hook-chunk-CNLMPHXT.mjs";
 import {
   registerReset
 } from "./token-goat-hook-chunk-BUOCULAM.mjs";
@@ -336,12 +341,12 @@ function buildGuidanceBody(fallbackToolClause, opts = {}) {
     '- searching for a *concept* rather than a literal string \u2192 `semantic "description"`',
     "- re-reading output you already captured \u2192 `bash-output`/`web-output`/`mcp-output` by ID",
     "- a directory listing or recursive wildcard walk to orient in an unfamiliar repo \u2192 `map --compact`",
-    "- pulling one value or subtree out of a JSON/YAML file (manifest, lockfile, spec, config) \u2192 `json-query file 'a.b.c'` / `yaml-query file 'a.b.c'`",
+    "- pulling one value or subtree out of a JSON/YAML/XML file (manifest, lockfile, spec, config) \u2192 `json-query file 'a.b.c'` / `yaml-query file 'a.b.c'` / `xml-query file 'a.b.c'`",
     "- opening an image to check its dimensions, format, or size \u2192 `image-meta file`",
     "- opening a screenshot, diagram, or scan to read the text in it \u2192 `image-text file`",
     "- opening a PDF or Office document \u2192 inspect its format first, then read a narrow slice: PDF `pdf-meta`/`pdf-outline` then `pdf-extract`; Word `docx-outline` then `docx-text`; PowerPoint `pptx-outline` then `pptx-slide`/`pptx-notes`; Excel `xlsx-sheets` then `xlsx-head`/`xlsx-range`/`xlsx-query`",
     "",
-    'Commands: `symbol NAME`, `read "file::symbol"`, `brief "file::symbol"`, `section "file::Heading"`, `semantic "description"`, `outline file`/`skeleton file`, `map --compact`, `refs file::symbol --callers`, `changed --symbol`, `config-get file KEY`, `json-query file \'a.b.c\'`/`yaml-query`, `json-outline file`/`yaml-outline`, `bash-output`/`web-output`/`mcp-output`, ' + (gdrive ? "`gdrive-sections <file-id>`, " : "") + "`image-meta file`/`image-text file`, `pdf-meta`/`pdf-outline`/`pdf-extract`, `docx-outline`/`docx-text`, `pptx-outline`/`pptx-slide`/`pptx-notes`/`pptx-text`, `xlsx-sheets`/`xlsx-head`/`xlsx-range`/`xlsx-query`.",
+    'Commands: `symbol NAME`, `read "file::symbol"`, `brief "file::symbol"`, `section "file::Heading"`, `semantic "description"`, `outline file`/`skeleton file`, `map --compact`, `refs file::symbol --callers`, `changed --symbol`, `config-get file KEY`, `json-query file \'a.b.c\'`/`yaml-query`/`xml-query`, `json-outline file`/`yaml-outline`/`xml-outline`, `bash-output`/`web-output`/`mcp-output`, ' + (gdrive ? "`gdrive-sections <file-id>`, " : "") + "`image-meta file`/`image-text file`, `pdf-meta`/`pdf-outline`/`pdf-extract`, `docx-outline`/`docx-text`, `pptx-outline`/`pptx-slide`/`pptx-notes`/`pptx-text`, `xlsx-sheets`/`xlsx-head`/`xlsx-range`/`xlsx-query`.",
     "",
     "Sub-agent briefs must carry this gate verbatim: a sub-agent inherits none of this context and its reads spend the same token budget.",
     "",
@@ -3211,10 +3216,11 @@ function logHintEmission(category, sessionId, correlator, compensateSelfResolve
   try {
     const db = getDb(globalDbPath());
     const resolved = correlator === null ? 1 : 0;
+    const actedOn = resolved === 1 && isSuppressionCategory(category) ? 1 : 0;
     const window = ACTED_ON_WINDOW + (compensateSelfResolve ? 1 : 0);
     db.prepare(
       `INSERT INTO hint_emissions (category, session_id, harness, correlator, emitted_at, resolved, acted_on, calls_remaining, bytes_emitted)
-       VALUES (@category, @sessionId, @harness, @correlator, @emittedAt, @resolved, 0, @callsRemaining, @bytesEmitted)`
+       VALUES (@category, @sessionId, @harness, @correlator, @emittedAt, @resolved, @actedOn, @callsRemaining, @bytesEmitted)`
     ).run({
       category,
       sessionId,
@@ -3222,6 +3228,7 @@ function logHintEmission(category, sessionId, correlator, compensateSelfResolve
       correlator,
       emittedAt: Date.now(),
       resolved,
+      actedOn,
       callsRemaining: correlator === null ? 0 : window,
       bytesEmitted
     });
@@ -3241,6 +3248,30 @@ function commandMentionsCorrelator(command, correlator) {
   }
   return false;
 }
+var SUPPRESSION_HINT_CATEGORIES = /* @__PURE__ */ new Set([
+  "read_reread_dedup",
+  "edit_reread_suggest"
+]);
+function isSuppressionCategory(category) {
+  return SUPPRESSION_HINT_CATEGORIES.has(category);
+}
+var EVENT_PATH_KEYS = ["file_path", "filePath", "notebook_path", "path"];
+function eventTargetText(event) {
+  if (event.toolName === "Bash") {
+    const c = event.toolInput["command"];
+    return typeof c === "string" ? c : "";
+  }
+  for (const key of EVENT_PATH_KEYS) {
+    const v = event.toolInput[key];
+    if (typeof v === "string" && v !== "") return v;
+  }
+  return "";
+}
+function isDefiance(correlator, target) {
+  if (target === "") return false;
+  if (TOKEN_GOAT_INVOCATION_RE.test(target)) return false;
+  return commandMentionsCorrelator(target, correlator);
+}
 function isActedOn(category, correlator, command) {
   if (!TOKEN_GOAT_INVOCATION_RE.test(command)) return false;
   if (category === "bash_recall") {
@@ -3252,10 +3283,29 @@ function resolvePendingHintsForEvent(event) {
   try {
     const db = getDb(globalDbPath());
     const command = event.toolName === "Bash" && typeof event.toolInput["command"] === "string" ? event.toolInput["command"] : "";
+    const target = eventTargetText(event);
     const pending = db.prepare(`SELECT id, category, correlator, calls_remaining FROM hint_emissions WHERE session_id = ? AND resolved = 0`).all(event.sessionId);
     for (const row of pending) {
       if (!isHintCategory(row.category) || row.correlator === null) {
-        db.prepare(`UPDATE hint_emissions SET resolved = 1 WHERE id = ?`).run(row.id);
+        const unobservable = isHintCategory(row.category) && isSuppressionCategory(row.category) ? 1 : 0;
+        db.prepare(`UPDATE hint_emissions SET acted_on = ?, resolved = 1 WHERE id = ?`).run(unobservable, row.id);
+        continue;
+      }
+      if (isSuppressionCategory(row.category)) {
+        if (isDefiance(row.correlator, target)) {
+          db.prepare(`UPDATE hint_emissions SET acted_on = 0, resolved = 1 WHERE id = ?`).run(row.id);
+          continue;
+        }
+        if (command !== "" && isActedOn(row.category, row.correlator, command)) {
+          db.prepare(`UPDATE hint_emissions SET acted_on = 1, resolved = 1 WHERE id = ?`).run(row.id);
+          continue;
+        }
+        const left = row.calls_remaining - 1;
+        if (left <= 0) {
+          db.prepare(`UPDATE hint_emissions SET acted_on = 1, resolved = 1 WHERE id = ?`).run(row.id);
+        } else {
+          db.prepare(`UPDATE hint_emissions SET calls_remaining = ? WHERE id = ?`).run(left, row.id);
+        }
         continue;
       }
       if (command !== "" && isActedOn(row.category, row.correlator, command)) {
@@ -3313,15 +3363,18 @@ function manualMarks(category) {
   }
 }
 function getHintStatsSummary() {
+  const probeThresholds = loadConfig().hints.backoff_thresholds.filter((t) => t > 0);
   return HINT_CATEGORIES.map((category) => {
     const { emitted, actedOn, bytesEmitted, legacyEmissions } = categoryStats(category);
     const marks = manualMarks(category);
+    const suppressed = shouldSuppress(category, "");
     return {
       category,
       emitted,
       actedOn: actedOn ?? 0,
       efficacyPct: emitted === 0 ? null : Math.round(1e3 * (actedOn ?? 0) / emitted) / 10,
-      suppressed: shouldSuppress(category, ""),
+      suppressed,
+      suppressionPermanent: suppressed && probeThresholds.length === 0,
       manualEffective: marks.effective,
       manualIneffective: marks.ineffective,
       bytesEmitted,
@@ -4057,7 +4110,7 @@ async function ocrImage(input) {
   const entryPath = resolveTesseractEntry();
   if (entryPath === null) return null;
   if (ocrBlockedOffline()) return null;
-  return new Promise((resolve9) => {
+  return new Promise((resolve10) => {
     let settled = false;
     let child;
     try {
@@ -4066,7 +4119,7 @@ async function ocrImage(input) {
       });
     } catch {
       _ocrUnavailableThisProcess = true;
-      resolve9(null);
+      resolve10(null);
       return;
     }
     const chunks = [];
@@ -4079,7 +4132,7 @@ async function ocrImage(input) {
         child.kill();
       } catch {
       }
-      resolve9(result);
+      resolve10(result);
     };
     const timer = setTimeout(() => finish(null, true), _ocrTimeoutMs);
     child.stdout?.on("data", (c) => chunks.push(c));
@@ -4204,11 +4257,11 @@ function statInfo(absPath) {
 function imageShrinkCacheDir() {
   return path10.join(tokenGoatHome(), "image_shrink_cache");
 }
-function shrinkCacheKey(originalPath, size, mtimeMs) {
-  return createHash2("sha256").update(`${originalPath}:${size}:${mtimeMs}`).digest("hex").slice(0, 16);
+function shrinkCacheKey(originalPath, size, mtimeMs, quality) {
+  return createHash2("sha256").update(`${originalPath}:${size}:${mtimeMs}:${quality}`).digest("hex").slice(0, 16);
 }
-function findCachedShrink(originalPath, size, mtimeMs) {
-  const key = shrinkCacheKey(originalPath, size, mtimeMs);
+function findCachedShrink(originalPath, size, mtimeMs, quality) {
+  const key = shrinkCacheKey(originalPath, size, mtimeMs, quality);
   const dir = imageShrinkCacheDir();
   const candidates = [
     { ext: ".webp", format: "webp" },
@@ -4220,11 +4273,11 @@ function findCachedShrink(originalPath, size, mtimeMs) {
   }
   return null;
 }
-function writeCachedShrink(originalPath, result, mtimeMs) {
+function writeCachedShrink(originalPath, result, mtimeMs, quality) {
   try {
     const dir = imageShrinkCacheDir();
     ensureDirSync(dir);
-    const key = shrinkCacheKey(originalPath, result.originalBytes, mtimeMs);
+    const key = shrinkCacheKey(originalPath, result.originalBytes, mtimeMs, quality);
     const ext = result.format === "jpeg" ? ".jpg" : ".webp";
     atomicWriteBytes(path10.join(dir, `token-goat-shrink-${key}${ext}`), result.data);
   } catch {
@@ -4278,7 +4331,8 @@ async function preReadImageHandler(event) {
   const stat2 = statInfo(filePath);
   if (stat2 === null) return passOutput();
   const size = stat2.size;
-  const cached = findCachedShrink(filePath, stat2.size, stat2.mtimeMs);
+  const quality = loadConfig().image_shrink.jpeg_quality;
+  const cached = findCachedShrink(filePath, stat2.size, stat2.mtimeMs, quality);
   if (cached !== null) {
     let cachedData;
     try {
@@ -4331,12 +4385,12 @@ async function preReadImageHandler(event) {
       return passOutput();
     }
   }
-  const result = await shrinkImage(input, { sizeThresholdBytes: 0 });
+  const result = await shrinkImage(input, { quality, sizeThresholdBytes: 0 });
   if (result === null) {
     recordStat("image_shrink_skipped");
     return passOutput();
   }
-  writeCachedShrink(filePath, result, stat2.mtimeMs);
+  writeCachedShrink(filePath, result, stat2.mtimeMs, quality);
   return finalizeShrinkResult(result, filePath);
 }
 registerHook("pre_tool_use", preReadImageHandler, { toolName: "Read" });
@@ -4398,7 +4452,7 @@ registerReset(() => {
   PIPELINE_RETRY_DELAY_MS = DEFAULT_PIPELINE_RETRY_DELAY_MS;
 });
 function sleep(ms) {
-  return new Promise((resolve9) => setTimeout(resolve9, ms));
+  return new Promise((resolve10) => setTimeout(resolve10, ms));
 }
 async function buildExtractorWithRetry(pipelineFn, modelName) {
   let lastError;
@@ -4948,6 +5002,7 @@ function trimToBudget(text, budgetTokens, command) {
     return text;
   }
   const lines2 = text.split("\n");
+  if (lines2.length > 1 && lines2[lines2.length - 1] === "") lines2.pop();
   const totalLines = lines2.length;
   const bodyBudget = Math.max(1, budgetTokens - markerMarginTokens);
   const charBudget = bodyBudget * 3;
@@ -6231,7 +6286,7 @@ var ResizeableBuffer = class {
   }
   toString(encoding) {
     if (encoding) {
-      return this.buf.slice(0, this.length).toString(encoding);
+      return this.buf.toString(encoding, 0, this.length);
     } else {
       return Uint8Array.prototype.slice.call(this.buf.slice(0, this.length));
     }
@@ -7483,14 +7538,19 @@ var transform = function(original_options = {}) {
           const obj = {};
           for (let i = 0, l = record.length; i < l; i++) {
             if (columns[i] === void 0 || columns[i].disabled) continue;
-            if (group_columns_by_name === true && obj[columns[i].name] !== void 0) {
+            if (group_columns_by_name === true && Object.hasOwn(obj, columns[i].name)) {
               if (Array.isArray(obj[columns[i].name])) {
                 obj[columns[i].name] = obj[columns[i].name].concat(record[i]);
               } else {
                 obj[columns[i].name] = [obj[columns[i].name], record[i]];
               }
             } else {
-              obj[columns[i].name] = record[i];
+              Object.defineProperty(obj, columns[i].name, {
+                value: record[i],
+                enumerable: true,
+                writable: true,
+                configurable: true
+              });
             }
           }
           if (raw === true || info2 === true) {
@@ -7917,6 +7977,7 @@ ${recall}`
     if (htmlResult.shouldBlock) return htmlResult;
   }
   const lines2 = content.split("\n");
+  if (lines2.length > 1 && lines2[lines2.length - 1] === "") lines2.pop();
   const preview = [
     "--- first 5 lines ---",
     ...lines2.slice(0, 5),
@@ -8532,7 +8593,8 @@ function isSessionArtifactFile(filePath) {
   if (/[/\\]tool-results[/\\][a-z0-9]+\.txt$/i.test(filePath)) return true;
   return false;
 }
-function sessionArtifactRecall(filePath) {
+function sessionArtifactRecall(rawPath) {
+  const filePath = displaySafePath(rawPath);
   return 'Use `token-goat bash-output --file "' + filePath + '" --tail 50` (or `--grep PATTERN`) to read a slice instead of the full file.';
 }
 function readIntToolInput(event, key) {
@@ -8599,7 +8661,8 @@ function estimateRequestedSlice(event, absPath) {
   if (scan.trustworthy) return { kind: "bytes", bytes: scan.bytes };
   return { kind: "unbounded" };
 }
-function describeSliceAdvice(slice, absPath) {
+function describeSliceAdvice(slice, rawAbsPath) {
+  const absPath = displaySafePath(rawAbsPath);
   if (slice.kind === "nearSingleLine") {
     return BYTE_RANGE_ADVICE(absPath);
   }
@@ -8758,6 +8821,7 @@ function preReadHandlerInner(event) {
   }
   if (filePath === void 0) return passOutput();
   const normalized = normalizePath(filePath);
+  const shown = displaySafePath(normalized);
   if (isNodeModulesPath(normalized)) {
     return denyOutput(
       "node_modules is typically noise; use npm ls, npm outdated, or npm audit instead for dependency info. To force access, use: token-goat read node_modules/package/file.js::symbol-name or token-goat section node_modules/package/file.js::heading"
@@ -8781,7 +8845,7 @@ function preReadHandlerInner(event) {
   const basename12 = path16.basename(normalized);
   if (isLockFile(basename12)) {
     return denyOutput(
-      'Lock files are rarely useful to read in full. Use `token-goat section "' + normalized + '::<section>"` to extract a specific dependency, or read the relevant manifest instead.'
+      'Lock files are rarely useful to read in full. Use `token-goat section "' + shown + '::<section>"` to extract a specific dependency, or read the relevant manifest instead.'
     );
   }
   if (normalized.toLowerCase().endsWith(".tsbuildinfo")) {
@@ -8805,13 +8869,13 @@ function preReadHandlerInner(event) {
   if (isTsConfigFile(basename12) && wasFileReadThisSession(normalized)) {
     recordActualRead(event, normalized);
     return quietContextOutput(
-      "Already read " + basename12 + '. Use `token-goat section "' + normalized + '::compilerOptions"` to extract compiler options, or `token-goat config-get ' + normalized + " compilerOptions.target` for a single value."
+      "Already read " + basename12 + '. Use `token-goat section "' + shown + '::compilerOptions"` to extract compiler options, or `token-goat config-get ' + shown + " compilerOptions.target` for a single value."
     );
   }
   if (isManifestFile(basename12) && wasFileReadThisSession(normalized)) {
     recordActualRead(event, normalized);
     return quietContextOutput(
-      "You've already read " + basename12 + '. Use `token-goat section "' + normalized + '::<field>"` or `token-goat config-get ' + normalized + " <key>` to extract just the value you need."
+      "You've already read " + basename12 + '. Use `token-goat section "' + shown + '::<field>"` or `token-goat config-get ' + shown + " <key>` to extract just the value you need."
     );
   }
   const skillName = detectSkillFile(normalized);
@@ -8840,7 +8904,7 @@ function preReadHandlerInner(event) {
         const savedBytes = Math.max(0, fullSize - compactBody.length);
         recordStat("session_hint", savedBytes, Math.round(savedBytes / 4));
         return denyOutput(
-          "Serving the extractive compact sidecar in place of the full file (source unchanged since the last `compact-doc` build):\n\n" + fenceUntrustedFileContent(compactBody) + '\n\nUse `token-goat compact-doc "' + normalized + '" --force` to rebuild it, or `token-goat compact-doc "' + normalized + '" --show` to view it directly. ' + editAnywayHint(normalized)
+          "Serving the extractive compact sidecar in place of the full file (source unchanged since the last `compact-doc` build):\n\n" + fenceUntrustedFileContent(compactBody) + '\n\nUse `token-goat compact-doc "' + shown + '" --force` to rebuild it, or `token-goat compact-doc "' + shown + '" --show` to view it directly. ' + editAnywayHint(normalized)
         );
       }
     }
@@ -8881,7 +8945,7 @@ function preReadHandlerInner(event) {
         const hintText = formatHeadingTree(headings, normalized);
         const headingTextsLower = new Set(headings.map((h) => h.text.trim().toLowerCase()));
         const wellKnown = getWellKnownSections(basename12).filter((s) => headingTextsLower.has(s.trim().toLowerCase()));
-        const wellKnownText = wellKnown.length > 0 ? "\nQuick access: " + wellKnown.map((s) => 'token-goat section "' + normalized + "::" + s + '"').join(" | ") : "";
+        const wellKnownText = wellKnown.length > 0 ? "\nQuick access: " + wellKnown.map((s) => 'token-goat section "' + shown + "::" + s + '"').join(" | ") : "";
         const changelogExtra = basename12.toLowerCase() === "changelog.md" ? extractChangelogVersionHint(fileContent, normalized) : "";
         let message = fenceUntrustedFileContent(hintText + changelogExtra) + wellKnownText;
         const slice = estimateRequestedSlice(event, normalized);
@@ -8905,7 +8969,7 @@ function preReadHandlerInner(event) {
     recordStat("session_hint", 0, 0);
     const isMainMemory = basename12.toLowerCase() === "memory.md";
     return denyOutput(
-      isMainMemory ? "MEMORY.md was read this session. Its content is in the compact manifest as 'session memory'." : normalized + ' was already read this session. Memory files rarely change mid-session. Use `token-goat section "' + normalized + '::SectionHeading"` to extract one section.'
+      isMainMemory ? "MEMORY.md was read this session. Its content is in the compact manifest as 'session memory'." : shown + ' was already read this session. Memory files rarely change mid-session. Use `token-goat section "' + shown + '::SectionHeading"` to extract one section.'
     );
   }
   if (/^\.improve-state-.*\.json$/.test(basename12) && wasFileReadThisSession(normalized)) {
@@ -8919,7 +8983,7 @@ function preReadHandlerInner(event) {
     recordActualRead(event, normalized);
     recordStat("session_hint", 0, 0);
     return denyOutput(
-      normalized + " was already read this session. Environment files rarely change mid-session. Use `token-goat config-get " + normalized + " KEY_NAME` to extract a specific variable."
+      shown + " was already read this session. Environment files rarely change mid-session. Use `token-goat config-get " + shown + " KEY_NAME` to extract a specific variable."
     );
   }
   if (isSessionArtifactFile(normalized)) {
@@ -8950,7 +9014,7 @@ function preReadHandlerInner(event) {
       recordActualRead(event, normalized);
       recordStat("session_hint", 0, 0);
       return denyOutput(
-        normalized + " was already read this session. " + sessionArtifactRecall(normalized)
+        shown + " was already read this session. " + sessionArtifactRecall(normalized)
       );
     }
     {
@@ -9009,7 +9073,7 @@ function preReadHandlerInner(event) {
         if (scanCrossSessionManifests(project.root, project.hash, normalized, ttlSecs)) {
           recordActualRead(event, normalized);
           return quietContextOutput(
-            "This file may have already been read by another agent/session working in this project recently. If you are a subagent continuing shared work, consider whether you already have this content from context, or use `token-goat read " + normalized + "::SymbolName` for a narrower slice instead of a full re-read."
+            "This file may have already been read by another agent/session working in this project recently. If you are a subagent continuing shared work, consider whether you already have this content from context, or use `token-goat read " + shown + "::SymbolName` for a narrower slice instead of a full re-read."
           );
         }
       }
@@ -9041,7 +9105,7 @@ function preReadHandlerInner(event) {
       if (/\.(md|mdx|markdown|rst)$/i.test(basename12)) {
         recordStat("session_hint", rereadCredit, Math.round(rereadCredit / 4));
         return denyOutput(
-          'Markdown file already read this session. Use `token-goat section "' + normalized + '::HeadingName"` to read one section. ' + editAnywayHint(normalized)
+          'Markdown file already read this session. Use `token-goat section "' + shown + '::HeadingName"` to read one section. ' + editAnywayHint(normalized)
         );
       }
       const isSourceExt = isSourceExtension(basename12);
@@ -9049,22 +9113,22 @@ function preReadHandlerInner(event) {
         recordStat("read_count_deny", rereadCredit, Math.round(rereadCredit / 4));
         recordStat("session_hint", rereadCredit, Math.round(rereadCredit / 4));
         return denyOutput(
-          "Read this file " + reads + ' times already \u2014 use `token-goat read "' + normalized + '::Symbol"`, `token-goat skeleton ' + normalized + "`, or `token-goat outline " + normalized + "` to pull just the part you need. " + editAnywayHint(normalized)
+          "Read this file " + reads + ' times already \u2014 use `token-goat read "' + shown + '::Symbol"`, `token-goat skeleton ' + shown + "`, or `token-goat outline " + shown + "` to pull just the part you need. " + editAnywayHint(normalized)
         );
       }
     }
-    const hint = _isDocFile(normalized) ? 'Use `token-goat section "' + normalized + '::SectionName"` to read one section.' : "Use token-goat read/section/symbol to re-read surgically.";
+    const hint = _isDocFile(normalized) ? 'Use `token-goat section "' + shown + '::SectionName"` to read one section.' : "Use token-goat read/section/symbol to re-read surgically.";
     if (config2.hints.reread_deny && !protectedRead && (rereadBytes >= config2.hints.reread_deny_min_bytes || reads >= 2)) {
       recordStat("session_hint", rereadCredit, Math.round(rereadCredit / 4));
       return denyOutput(
-        normalized + " was already read this session (" + reads + " " + plural + "). " + hint + " " + editAnywayHint(normalized)
+        shown + " was already read this session (" + reads + " " + plural + "). " + hint + " " + editAnywayHint(normalized)
       );
     }
     if (!isWithinQuietHours(config2.hints.quiet_hours)) {
       recordStat("session_hint", 0, 0);
     }
     return quietContextOutput(
-      "Note: " + normalized + " was already read this session (" + reads + " " + plural + "). " + hint
+      "Note: " + shown + " was already read this session (" + reads + " " + plural + "). " + hint
     );
   }
   const size = statSize(normalized);
@@ -9077,12 +9141,12 @@ function preReadHandlerInner(event) {
     }
     const kb = toKB(size);
     const config2 = loadConfig();
-    const hint = _isDocFile(normalized) ? 'Use `token-goat section "' + normalized + '::SectionName"` to read one section.' : "Consider token-goat skeleton or token-goat section.";
+    const hint = _isDocFile(normalized) ? 'Use `token-goat section "' + shown + '::SectionName"` to read one section.' : "Consider token-goat skeleton or token-goat section.";
     if (gateSize >= largeFileDenyBytes()) {
       const denyCredit = Math.min(size, PER_FILE_COUNTERFACTUAL_CEILING);
       recordStat("session_hint", denyCredit, Math.round(denyCredit / 4));
       return denyOutput(
-        normalized + " is very large (" + kb + "KB). " + hint + " " + describeSliceAdvice(slice, normalized) + " " + editAnywayHint(normalized)
+        shown + " is very large (" + kb + "KB). " + hint + " " + describeSliceAdvice(slice, normalized) + " " + editAnywayHint(normalized)
       );
     }
     recordActualRead(event, normalized);
@@ -9096,7 +9160,7 @@ function preReadHandlerInner(event) {
       recordStat("session_hint", 0, 0);
     }
     return quietContextOutput(
-      "Note: " + normalized + " is large (" + kb + "KB). " + hint + contextPressureAdvisorySuffix()
+      "Note: " + shown + " is large (" + kb + "KB). " + hint + contextPressureAdvisorySuffix()
     );
   }
   const fileTypeExt = path16.extname(normalized).slice(1).toLowerCase();
@@ -9144,16 +9208,19 @@ function estimateTruncatedLineCount(normalized) {
   }
   return Infinity;
 }
-function editAnywayHint(normalized) {
+function editAnywayHint(rawPath) {
+  const normalized = displaySafePath(rawPath);
   return 'To edit it anyway, use `token-goat replace "' + normalized + '" --old-b64 <base64> --new-b64 <base64>` (preferred \u2014 no temp files needed) or `--old-from <oldfile> --new-from <newfile>` for a snippet edit, or `token-goat write-file "' + normalized + "\" --b64 <base64>` (or `--from <newfile>`) to rewrite the whole file \u2014 Read/Edit's own precondition can't be satisfied after this deny.";
 }
-function truncatedReadDenyMessage(normalized) {
+function truncatedReadDenyMessage(rawPath) {
+  const normalized = displaySafePath(rawPath);
   return 'File was truncated on last read (>33K tokens). Use `token-goat skeleton "' + normalized + '"` for structure or `token-goat read "' + normalized + '::SymbolName"` for one function. ' + editAnywayHint(normalized);
 }
 function postReadHandlerInner(event) {
   const filePath = getFilePath(event);
   if (filePath === void 0) return passOutput();
   const normalized = normalizePath(filePath);
+  const shown = displaySafePath(normalized);
   const respText = extractReadOutput(event.raw);
   if (respText.includes("[Truncated:") || respText.includes("Truncated: PARTIAL view")) {
     markFileTruncated(normalized);
@@ -9174,7 +9241,7 @@ function postReadHandlerInner(event) {
     try {
       const cwd = getCwd(event) ?? process.cwd();
       const project = findProject(cwd) ?? makeProjectAt(cwd);
-      const source = fs18.readFileSync(normalized, "utf8");
+      const source = decodeSource(fs18.readFileSync(normalized));
       recordEvidence({ projectRoot: project.root, source: normalized, representation: "file", text: source });
     } catch {
     }
@@ -9210,7 +9277,7 @@ function postReadHandlerInner(event) {
         if (lineCount >= minLines && meetsSavingsFloor(sz)) {
           recordStat("session_hint", 0, 0);
           return quietContextOutput(
-            normalized + " is " + lineCount + ' lines. Use `token-goat skeleton "' + normalized + '"` or `token-goat outline "' + normalized + '"` for structural navigation instead of a future full re-read.'
+            shown + " is " + lineCount + ' lines. Use `token-goat skeleton "' + shown + '"` or `token-goat outline "' + shown + '"` for structural navigation instead of a future full re-read.'
           );
         }
       }
@@ -9688,9 +9755,12 @@ function profileCsv(content, opts = {}) {
 }
 function formatCsvProfile(profiles) {
   return profiles.map((p) => {
-    const lines2 = [`${p.name}  (${p.inferredType})`, `  nulls: ${p.nullCount}  distinct: ${p.distinctCount}`];
-    if (p.min !== void 0) lines2.push(`  range: ${p.min} .. ${p.max}`);
-    if (p.topValues !== void 0) lines2.push(`  values: ${p.topValues.map((t) => `${t.value} (${t.count})`).join(", ")}`);
+    const lines2 = [
+      `${displaySafeText(p.name)}  (${p.inferredType})`,
+      `  nulls: ${p.nullCount}  distinct: ${p.distinctCount}`
+    ];
+    if (p.min !== void 0) lines2.push(`  range: ${displaySafeText(p.min)} .. ${displaySafeText(p.max ?? "")}`);
+    if (p.topValues !== void 0) lines2.push(`  values: ${p.topValues.map((t) => `${displaySafeText(t.value)} (${t.count})`).join(", ")}`);
     return lines2.join("\n");
   }).join("\n\n");
 }
@@ -10607,7 +10677,7 @@ function extractHtml(content, filePath) {
     }
   }
   sections.sort((a, b) => a.line - b.line);
-  const totalLines = code.split("\n").length;
+  const totalLines = countContentLines(code);
   assignFlatEndLines(sections, totalLines);
   const seenId = /* @__PURE__ */ new Set();
   const seenClass = /* @__PURE__ */ new Set();
@@ -10710,7 +10780,7 @@ function extractLiquid(content, filePath, relPath) {
     const stem = path18.basename(resolvedRel, path18.extname(resolvedRel));
     symbols.push({ filePath, name: stem, kind: "liquid_section_file", lineStart: 1, lineEnd: 1, body: "", docstring: "", parent: "" });
   }
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   for (const hm of findHtmlHeadingMatches(content)) {
     if (hm.heading) {
       const line = offsetToLine(lineIndex, hm.offset);
@@ -11687,12 +11757,64 @@ function extractZig(content, filePath) {
 
 // src/languages/r.ts
 var FUNC_ASSIGN_RE = /^([A-Za-z_][A-Za-z0-9_.]*)\s*(?:<-|=)\s*(?:function|\\)\s*\(/;
-var SETCLASS_RE = /setClass\s*\(\s*["']([A-Za-z_][A-Za-z0-9_.]*)/;
-var SETMETHOD_RE = /setMethod\s*\(\s*["']([A-Za-z_][A-Za-z0-9_.]*)/;
+var SETCLASS_RE = /^(?:[A-Za-z_][A-Za-z0-9_.]*\s*(?:<-|=)\s*)?setClass\s*\(\s*["']([A-Za-z_][A-Za-z0-9_.]*)/;
+var SETMETHOD_RE = /^(?:[A-Za-z_][A-Za-z0-9_.]*\s*(?:<-|=)\s*)?setMethod\s*\(\s*["']([A-Za-z_][A-Za-z0-9_.]*)/;
+function matchingParenIndex(content, openIndex) {
+  let depth = 0;
+  let quote = null;
+  for (let i = openIndex; i < content.length; i++) {
+    const ch = content[i];
+    if (quote !== null) {
+      if (ch === "\\") {
+        i++;
+        continue;
+      }
+      if (ch === quote) quote = null;
+      continue;
+    }
+    if (ch === "#") {
+      while (i < content.length && content[i] !== "\n") i++;
+      continue;
+    }
+    if (ch === '"' || ch === "'" || ch === "`") {
+      quote = ch;
+      continue;
+    }
+    if (ch === "(") depth++;
+    else if (ch === ")") {
+      depth--;
+      if (depth === 0) return i;
+    }
+  }
+  return null;
+}
+function bracedBodyEndLine(content, lineIndex, parenIndex, totalLines, fallback) {
+  const close = matchingParenIndex(content, parenIndex);
+  if (close === null) return fallback;
+  let j = close + 1;
+  while (j < content.length) {
+    const ch = content[j];
+    if (ch === "#") {
+      while (j < content.length && content[j] !== "\n") j++;
+      continue;
+    }
+    if (ch !== " " && ch !== "	" && ch !== "\r" && ch !== "\n") break;
+    j++;
+  }
+  if (content[j] !== "{") return fallback;
+  return findMatchingBraceEndLine(content, j, totalLines, lineIndex, "#");
+}
+function callEndLine(content, lineIndex, parenIndex, fallback) {
+  const close = matchingParenIndex(content, parenIndex);
+  return close === null ? fallback : offsetToLine(lineIndex, close);
+}
 function extractR(content, filePath) {
   const symbols = [];
   const imports = [];
   const lines2 = content.split(/\r?\n/);
+  const lineIndex = buildLineIndex(content);
+  const totalLines = countContentLines(content);
+  const spanBody = (startLine, endLine) => lines2.slice(startLine - 1, endLine).join("\n");
   for (let i = 0; i < lines2.length; i++) {
     const rawLine = lines2[i] ?? "";
     const lineNum = i + 1;
@@ -11705,17 +11827,21 @@ function extractR(content, filePath) {
     if (!isIndented) {
       const fm = FUNC_ASSIGN_RE.exec(stripped);
       if (fm) {
-        symbols.push(makeLineSymbol(filePath, fm[1] ?? "", "function", lineNum, stripped.slice(0, 200), void 0, lines2, "hash"));
+        const parenIndex = (lineIndex[i] ?? 0) + fm[0].length - 1;
+        const endLine = bracedBodyEndLine(content, lineIndex, parenIndex, totalLines, lineNum);
+        symbols.push(makeSpanSymbol(filePath, fm[1] ?? "", "function", { startLine: lineNum, endLine, body: spanBody(lineNum, endLine) }, void 0, lines2, "hash"));
         continue;
       }
       const cm = SETCLASS_RE.exec(stripped);
       if (cm) {
-        symbols.push(makeLineSymbol(filePath, cm[1] ?? "", "class", lineNum, stripped.slice(0, 200), void 0, lines2, "hash"));
+        const endLine = callEndLine(content, lineIndex, (lineIndex[i] ?? 0) + (cm.index + cm[0].indexOf("(")), lineNum);
+        symbols.push(makeSpanSymbol(filePath, cm[1] ?? "", "class", { startLine: lineNum, endLine, body: spanBody(lineNum, endLine) }, void 0, lines2, "hash"));
         continue;
       }
       const mm = SETMETHOD_RE.exec(stripped);
       if (mm) {
-        symbols.push(makeLineSymbol(filePath, mm[1] ?? "", "function", lineNum, stripped.slice(0, 200), void 0, lines2, "hash"));
+        const endLine = callEndLine(content, lineIndex, (lineIndex[i] ?? 0) + (mm.index + mm[0].indexOf("(")), lineNum);
+        symbols.push(makeSpanSymbol(filePath, mm[1] ?? "", "function", { startLine: lineNum, endLine, body: spanBody(lineNum, endLine) }, void 0, lines2, "hash"));
       }
     }
   }
@@ -11782,7 +11908,7 @@ function extractGraphql(content, filePath) {
     }
   }
   const stripped = stripHashComments(descriptionsStripped);
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(stripped);
   for (const m of stripped.matchAll(TYPE_RE)) {
     const keyword = m.groups?.["keyword"] ?? "";
@@ -12058,7 +12184,7 @@ function extractSql(content, filePath) {
   const sections = [];
   const seen = /* @__PURE__ */ new Set();
   const emit2 = makeSymbolEmitter(symbols, sections, seen, filePath, MAX_SYMBOLS3, MAX_HEADING_LEN2);
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(content);
   const noStrings = stripSqlStringLiterals(content);
   const singleLineEndLines = /* @__PURE__ */ new Map();
@@ -12260,7 +12386,7 @@ function extractMakefile(content, filePath) {
   const seen = /* @__PURE__ */ new Set();
   const emit2 = makeSymbolEmitter(symbols, sections, seen, filePath, MAX_SYMBOLS5, MAX_HEADING_LEN3);
   const stripped = stripComments(content);
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(stripped);
   const { noContinuation: strippedNoContinuation, forTargets: strippedForTargets } = maskContinuationAndDefines(stripped);
   for (const m of strippedForTargets.matchAll(TARGET_RE)) {
@@ -12340,7 +12466,7 @@ function extractProto(content, filePath) {
   const imports = [];
   const emit2 = makeSymbolEmitter(symbols, sections, seen, filePath, MAX_SYMBOLS6, MAX_HEADING_LEN4);
   const stripped = stripComments2(content);
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(stripped);
   const blockEndLines = /* @__PURE__ */ new Map();
   for (const m of stripped.matchAll(IMPORT_RE4)) {
@@ -12473,7 +12599,7 @@ function extractTerraform(content, filePath) {
   const seen = /* @__PURE__ */ new Set();
   const emit2 = makeSymbolEmitter(symbols, sections, seen, filePath, MAX_SYMBOLS7, MAX_HEADING_LEN5);
   const stripped = stripComments3(maskHeredocs(content));
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(stripped);
   const blockEndLines = /* @__PURE__ */ new Map();
   const matches = [
@@ -13271,8 +13397,8 @@ function extractLwcJavaScript(content, filePath) {
   const sourceLines = lines(content);
   const bundle = bundleName(filePath);
   const symbols = [
-    symbol(filePath, bundle, "lwc_bundle", 1, sourceLines.length),
-    symbol(filePath, lwcTagAlias(bundle), "lwc_component_alias", 1, sourceLines.length)
+    symbol(filePath, bundle, "lwc_bundle", 1, countContentLines(content)),
+    symbol(filePath, lwcTagAlias(bundle), "lwc_component_alias", 1, countContentLines(content))
   ];
   const refs = [];
   const commentFree = stripJsComments(content);
@@ -13370,10 +13496,9 @@ function attributeRefs(refs, content, filePath, attribute, split = false) {
 function extractSalesforceMarkup(content, filePath) {
   const normalized = filePath.replaceAll("\\", "/");
   const extension = path20.posix.extname(normalized).toLowerCase();
-  const sourceLines = lines(content);
   const kind = MARKUP_KIND[extension] ?? "salesforce_markup";
   const symbols = [
-    symbol(filePath, markupArtifactName(normalized, extension), kind, 1, sourceLines.length)
+    symbol(filePath, markupArtifactName(normalized, extension), kind, 1, countContentLines(content))
   ];
   const refs = [];
   const isAura = [".cmp", ".app", ".evt", ".intf", ".design", ".auradoc", ".tokens"].includes(extension);
@@ -13525,7 +13650,7 @@ function componentSymbol(filePath, name, kind, totalLines) {
   return { filePath, name, kind, lineStart: 1, lineEnd: totalLines, body: "", docstring: "", parent: "" };
 }
 function extractVue(content, filePath) {
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(content);
   const name = componentName(filePath);
   const symbols = [componentSymbol(filePath, name, "vue_component", totalLines)];
@@ -13540,7 +13665,7 @@ function extractVue(content, filePath) {
   return finalize(symbols, refs);
 }
 function extractSvelte(content, filePath) {
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(content);
   const name = componentName(filePath);
   const symbols = [componentSymbol(filePath, name, "svelte_component", totalLines)];
@@ -13573,7 +13698,7 @@ function detectAstroFrontmatter(content) {
   return null;
 }
 function extractAstro(content, filePath) {
-  const totalLines = content.split("\n").length;
+  const totalLines = countContentLines(content);
   const lineIndex = buildLineIndex(content);
   const name = componentName(filePath);
   const symbols = [componentSymbol(filePath, name, "astro_component", totalLines)];
@@ -13788,6 +13913,12 @@ var TSJS_KIND_BY_TYPE = /* @__PURE__ */ new Map([
   ["method_signature", "method"],
   ["property_signature", "var"],
   ["abstract_method_signature", "method"],
+  // `declare function f(): void` parses as a `function_signature` inside an
+  // ambient_declaration -- a distinct node type from `function_declaration`, which always
+  // carries a body. Without an entry here every ambient function in a .d.ts file was
+  // missing from the index entirely, the same container-drop shape as the module entries
+  // below rather than a wrong span.
+  ["function_signature", "function"],
   // `namespace Foo { ... }` (and the legacy `module Foo { ... }` synonym) parses as
   // `internal_module`; `declare module "some-string" { ... }` (an ambient module declaration,
   // common in .d.ts files) parses as `module` -- a distinct node type from either. Neither had a
@@ -13836,15 +13967,41 @@ function nodeName(node) {
   if (named !== null) return named.text;
   return null;
 }
+var SPEC_DECLARATION_OWNER = /* @__PURE__ */ new Map([
+  ["variable_declarator", /* @__PURE__ */ new Set(["lexical_declaration", "variable_declaration"])],
+  ["var_spec", /* @__PURE__ */ new Set(["var_declaration"])],
+  ["const_spec", /* @__PURE__ */ new Set(["const_declaration"])],
+  ["type_spec", /* @__PURE__ */ new Set(["type_declaration"])]
+]);
+var PREFIX_WRAPPER_TYPES = /* @__PURE__ */ new Set(["export_statement", "ambient_declaration"]);
+function widenToDeclaration(node) {
+  let widened = node;
+  const owner = SPEC_DECLARATION_OWNER.get(widened.type);
+  if (owner !== void 0) {
+    const decl = widened.parent;
+    if (decl === null || !owner.has(decl.type)) return widened;
+    let specs = 0;
+    for (const c of decl.namedChildren) if (c.type === widened.type) specs++;
+    if (specs !== 1) return widened;
+    if (decl.startPosition.row !== widened.startPosition.row) return widened;
+    widened = decl;
+  }
+  for (; ; ) {
+    const parent = widened.parent;
+    if (parent === null || !PREFIX_WRAPPER_TYPES.has(parent.type)) return widened;
+    widened = parent;
+  }
+}
 function makeSymbol(filePath, name, kind, node, lines2, style) {
-  const lineStart = node.startPosition.row + 1;
+  const ranged = widenToDeclaration(node);
+  const lineStart = ranged.startPosition.row + 1;
   return {
     filePath,
     name,
     kind,
     lineStart,
-    lineEnd: node.endPosition.row + 1,
-    body: node.text,
+    lineEnd: ranged.endPosition.row + 1,
+    body: ranged.text,
     docstring: lines2 !== void 0 && style !== void 0 ? precedingDocComment(lines2, lineStart, style) : "",
     parent: ""
   };
@@ -13883,13 +14040,23 @@ function extractTsJsSymbols(root, filePath, lines2) {
           out.push(makeSymbol(filePath, name, kind, node, lines2, "c"));
         } else {
           const lineStart = decorators[0].startPosition.row + 1;
+          const decoratedEnd = widenToDeclaration(node).endPosition.row + 1;
           out.push({
             filePath,
             name,
             kind,
             lineStart,
-            lineEnd: node.endPosition.row + 1,
-            body: [...decorators, node].map((n) => n.text).join("\n"),
+            lineEnd: decoratedEnd,
+            // Read the body off the file rather than gluing the decorator and the node
+            // together with a newline: `@dec export class X {}` has no newline between
+            // them, and the glued form both invents one and drops the `export` that sits
+            // between the two nodes. A decorated declaration yields one symbol, so taking
+            // its whole span cannot fan out.
+            // The trailing replace keeps a convention the rest of the index follows: a
+            // tree-sitter node never carries the indentation of its own first line,
+            // because it starts at the first real character. Reading the span off the
+            // file would otherwise make decorated symbols the one shape that does.
+            body: lines2.slice(lineStart - 1, decoratedEnd).join("\n").replace(/^[ \t]+/, ""),
             docstring: precedingDocComment(lines2, lineStart, "c"),
             parent: ""
           });
@@ -13906,8 +14073,11 @@ function extractTsJsSymbols(root, filePath, lines2) {
           const isFn = value !== null && (value.type === "arrow_function" || value.type === "function_expression" || value.type === "function");
           out.push(makeSymbol(filePath, name.text, isFn ? "function" : "variable", child, lines2, "c"));
         } else {
-          for (const bound of collectPatternBindings(name)) {
-            out.push(makeSymbol(filePath, bound, "variable", child, lines2, "c"));
+          const bindings = collectPatternBindings(name);
+          const elideBodies = bindings.length > 1 && bindings.length * child.text.length > MAX_SYMBOL_BODY_CHARS;
+          for (const bound of bindings) {
+            const sym = makeSymbol(filePath, bound, "variable", child, lines2, "c");
+            out.push(elideBodies ? { ...sym, body: "" } : sym);
           }
         }
       }
@@ -15419,7 +15589,7 @@ function indexFileSync(filePath, dbPath = globalDbPath(), preReadBytes) {
       throw err;
     }
   }
-  const content = raw.toString("utf8");
+  const content = decodeSource(raw);
   const { symbols, refs } = parseContent(content, filePath, language);
   writeParseResult(filePath, raw, { symbols, refs, language, duration: 0 }, dbPath);
 }
@@ -15444,6 +15614,19 @@ var UNAVAILABLE_EMBED_SHA_PREFIX = "unavailable:";
 function unavailableEmbedSha(sha) {
   return UNAVAILABLE_EMBED_SHA_PREFIX + sha;
 }
+function indexedPathSpellingIsStale(storedPath, absPath) {
+  if (!isCaseInsensitiveFs()) return false;
+  const stored = normalizePath(storedPath);
+  const candidate = normalizePath(path22.resolve(absPath));
+  if (foldPath(stored) !== foldPath(candidate)) return false;
+  let real;
+  try {
+    real = normalizePath(fs21.realpathSync.native(absPath));
+  } catch {
+    return false;
+  }
+  return real !== stored && foldPath(real) === foldPath(stored);
+}
 function isEmbedFresh(storedEmbedSha, sha, embeddingsEnabled, depsAvailable) {
   if (storedEmbedSha === void 0) return false;
   if (!embeddingsEnabled) return storedEmbedSha === disabledEmbedSha(sha);
@@ -15488,7 +15671,7 @@ async function indexFileEmbeddings(filePath, dbPath = globalDbPath(), sha, onErr
   }
   let content;
   try {
-    content = await fs21.promises.readFile(filePath, "utf8");
+    content = decodeSource(await fs21.promises.readFile(filePath));
   } catch {
     return;
   }
@@ -15626,6 +15809,41 @@ function pruneSystemTempFiles(dbPath = globalDbPath()) {
   const db = getDb(dbPath);
   return removeFilesBestEffort(db, findSystemTempFiles(dbPath));
 }
+function findOrphanedChunkPaths(dbPath = globalDbPath()) {
+  return orphanedChunkGroups(getDb(dbPath)).map((g) => g.representative);
+}
+function orphanedChunkGroups(db) {
+  const known = new Set(
+    db.prepare("SELECT DISTINCT path FROM files").all().map(
+      (r) => foldPath(normalizePath(r.path))
+    )
+  );
+  const rows = db.prepare("SELECT DISTINCT file_path FROM chunks").all();
+  const byFolded = /* @__PURE__ */ new Map();
+  for (const { file_path: raw } of rows) {
+    const folded = foldPath(normalizePath(raw));
+    if (known.has(folded)) continue;
+    const group = byFolded.get(folded);
+    if (group === void 0) byFolded.set(folded, { representative: raw, spellings: [raw] });
+    else group.spellings.push(raw);
+  }
+  return [...byFolded.values()];
+}
+function pruneOrphanedChunks(dbPath = globalDbPath()) {
+  const db = getDb(dbPath);
+  const removed = [];
+  const run = db.transaction(() => {
+    for (const group of orphanedChunkGroups(db)) {
+      try {
+        for (const spelling of group.spellings) deleteFileEmbeddings(db, spelling);
+        removed.push(group.representative);
+      } catch {
+      }
+    }
+  });
+  run.immediate();
+  return removed;
+}
 function recordKnownRoot(filePath, dbPath = globalDbPath()) {
   const project = findProject(path23.dirname(filePath));
   if (project === null || isTooShallowToPrune(project.root)) return;
@@ -15680,7 +15898,8 @@ function sweepKnownRoots(dbPath = globalDbPath(), opts) {
     prunedRows += removeDeletedFilesBestEffort(db, deletable).length;
     prunedRoots.push(root);
   }
-  return { prunedRows, prunedRoots, flaggedRoots };
+  const prunedOrphanChunkPaths = pruneOrphanedChunks(dbPath);
+  return { prunedRows, prunedRoots, flaggedRoots, prunedOrphanChunkPaths };
 }
 var KNOWN_ROOT_RECORD_MIN_INTERVAL_MS = 60 * 60 * 1e3;
 function knownRootRecordMarkerPath(dir, filePath) {
@@ -15821,11 +16040,25 @@ function pidFileIsWithinStartupGrace(dir) {
     return false;
   }
 }
+var ENCODED_LINE_MARKER = "!";
+function encodeDirtyQueueLine(absPath) {
+  const needsEncoding = /[\r\n]/.test(absPath) || absPath !== absPath.trim();
+  return needsEncoding ? ENCODED_LINE_MARKER + JSON.stringify(absPath) : absPath;
+}
+function decodeDirtyQueueLine(line) {
+  if (!line.startsWith(ENCODED_LINE_MARKER)) return line;
+  try {
+    const decoded = JSON.parse(line.slice(ENCODED_LINE_MARKER.length));
+    return typeof decoded === "string" ? decoded : line;
+  } catch {
+    return line;
+  }
+}
 function parseDirtyQueueLines(raw) {
   const seen = /* @__PURE__ */ new Set();
   const out = [];
   for (const line of raw.split("\n")) {
-    const trimmed = line.trim();
+    const trimmed = decodeDirtyQueueLine(line.trim());
     if (trimmed === "") continue;
     const normalized = normalizePath(trimmed);
     const dedupeKey = foldPath(normalized);
@@ -15913,10 +16146,10 @@ function embedFileSerialized(absPath, dbPath, sha) {
       activeEmbedSlots += 1;
       return dispatchEmbed();
     }
-    return new Promise((resolve9) => {
+    return new Promise((resolve10) => {
       embedSlotWaiters.push(() => {
         activeEmbedSlots += 1;
-        resolve9(dispatchEmbed());
+        resolve10(dispatchEmbed());
       });
     });
   };
@@ -15970,7 +16203,7 @@ function appendToDirtyQueue(dir, absPath) {
       if (existing.length > 0 && !existing.endsWith("\n")) leadingNewline = "\n";
     } catch {
     }
-    fs23.appendFileSync(queuePath, `${leadingNewline}${absPath}
+    fs23.appendFileSync(queuePath, `${leadingNewline}${encodeDirtyQueueLine(absPath)}
 `);
   } catch {
   }
@@ -15988,7 +16221,7 @@ function makeIndexer(dbPath) {
         return true;
       }
       const entry = getFileEntry(absPath, dbPath);
-      const parseUnchanged = entry?.sha === sha;
+      const parseUnchanged = entry?.sha === sha && !(entry !== null && indexedPathSpellingIsStale(entry.filePath, absPath));
       if (!parseUnchanged) {
         indexFileSync(absPath, dbPath);
       }
@@ -16021,7 +16254,7 @@ function processDirtyBatch(paths, index = makeIndexer(globalDbPath()), remove =
     if (!p) continue;
     writeDrainHeartbeat(dir);
     if (isUnderBlockedRoot(p, blockedRoots)) continue;
-    if (!fs23.existsSync(p)) {
+    if (fileIsAbsent(p)) {
       remove(p);
       continue;
     }
@@ -16253,6 +16486,12 @@ function claimWorkerPidFile(dir, pid) {
   if (existingPid !== null && pidAlive(existingPid) && (hasFreshWorkerHeartbeat(dir, existingPid) || pidFileIsWithinStartupGrace(dir))) {
     return false;
   }
+  if (existingPid !== null && pidAlive(existingPid) && existingPid !== pid && existingPid !== process.pid) {
+    try {
+      process.kill(existingPid, "SIGTERM");
+    } catch {
+    }
+  }
   try {
     fs23.rmSync(pidPath, { force: true });
   } catch {
@@ -16352,7 +16591,7 @@ async function runWorkerLoop(dir, pollIntervalMs, shouldStop = () => false) {
       lastKnownRootsSweepMs = Date.now();
     }
     if (shouldStop()) break;
-    await new Promise((resolve9) => setTimeout(resolve9, pollIntervalMs));
+    await new Promise((resolve10) => setTimeout(resolve10, pollIntervalMs));
   }
 }
 function runDetachedWorkerDaemon() {
@@ -16391,7 +16630,7 @@ function appendDirtyPath(normalizedPath2) {
     if (existing.length > 0 && !existing.endsWith("\n")) leadingNewline = "\n";
   } catch {
   }
-  fs24.appendFileSync(queuePath, `${leadingNewline}${normalizedPath2}
+  fs24.appendFileSync(queuePath, `${leadingNewline}${encodeDirtyQueueLine(normalizedPath2)}
 `);
 }
 function enqueueDirtyPathSafe(filePath, opts) {
@@ -16482,7 +16721,7 @@ import * as readline from "node:readline";
 async function defaultConfirm(question) {
   const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
   try {
-    const answer = await new Promise((resolve9) => rl.question(question, resolve9));
+    const answer = await new Promise((resolve10) => rl.question(question, resolve10));
     return /^y(es)?$/i.test(answer.trim());
   } finally {
     rl.close();
@@ -17533,6 +17772,7 @@ export {
   tomlBracketDelta,
   isParseSkipEligible,
   indexFileSync,
+  indexedPathSpellingIsStale,
   isEmbedFresh,
   indexFileEmbeddings,
   removeFileFromIndex,
@@ -17540,6 +17780,8 @@ export {
   pruneBlockedRoot,
   findSystemTempFiles,
   pruneSystemTempFiles,
+  findOrphanedChunkPaths,
+  pruneOrphanedChunks,
   recordKnownRootThrottled,
   WORKER_HEARTBEAT_STALE_MS,
   dirtyQueuePathFor,