docdex 0.2.59 → 0.2.61

package/CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## 0.2.61
+- Add the optional personal-preferences memory subsystem with local capture, background digestion, and packaged HTTP/CLI/MCP controls for status, search, processing, export, redaction, deletion, and purge flows.
+- Align the packaged personal-preferences surface with the top-level `[personal_preferences]` config, richer lineage/materialization, review and retention controls, bounded chat-context injection, and supported-client transcript scanning.
+- Harden installer-managed client config rewrites so whitespace-padded Docdex keys and section names are normalized instead of duplicated on reinstall.
+
+## 0.2.60
+- Deduplicate installer-managed Docdex client config on reinstall: JSON client configs now collapse stale `docdex` entries, Codex TOML converges to one canonical Docdex entry, and packaged Docdex instruction blocks replace older Codex/Gemini/Claude prompt blocks instead of duplicating them.
+- Update the packaged daemon dependency set to remove the vulnerable `rustls-webpki` chain that caused the nightly security audit failure.
+
 ## 0.2.58
 - Export Docdex delegation savings in hourly mswarm telemetry packages and expose matching runtime/admin mswarm summaries for frontend visibility.
 

package/assets/agents.md

@@ -1,4 +1,4 @@
----- START OF DOCDEX INFO V0.2.59 ----
+---- START OF DOCDEX INFO V0.2.61 ----
 Docdex URL: http://127.0.0.1:28491
 Use this base URL for Docdex HTTP endpoints.
 Health check endpoint: `GET /healthz` (not `/v1/health`).

package/lib/postinstall_setup.js

@@ -666,8 +666,17 @@ function stripLegacyDocdexBodySegment(segment, body) {
   const normalizedSegment = String(segment || "").replace(/\r\n/g, "\n");
   const normalizedBody = String(body || "").replace(/\r\n/g, "\n");
   if (!normalizedBody.trim()) return normalizedSegment;
-  const re = new RegExp(`\\n?${escapeRegExp(normalizedBody)}\\n?`, "g");
-  return normalizedSegment.replace(re, "\n").replace(/\n{3,}/g, "\n\n");
+  let result = normalizedSegment;
+  let index = result.indexOf(normalizedBody);
+  while (index !== -1) {
+    let start = index;
+    let end = index + normalizedBody.length;
+    if (start > 0 && result[start - 1] === "\n") start -= 1;
+    if (end < result.length && result[end] === "\n") end += 1;
+    result = `${result.slice(0, start)}\n${result.slice(end)}`;
+    index = result.indexOf(normalizedBody);
+  }
+  return result.replace(/\n{3,}/g, "\n\n");
 }
 
 function stripLegacyDocdexBody(text, body) {
@@ -1082,6 +1091,7 @@ function upsertMcpServerJson(pathname, url, options = {}) {
   const { value } = readJson(pathname);
   if (typeof value !== "object" || value == null || Array.isArray(value)) return false;
   const root = value;
+  const before = JSON.stringify(root);
   const extra =
     options &&
     typeof options === "object" &&
@@ -1090,9 +1100,44 @@ function upsertMcpServerJson(pathname, url, options = {}) {
     !Array.isArray(options.extra)
       ? options.extra
       : {};
-  const extraEntries = Object.entries(extra);
-  const matchesExtras = (entry) =>
-    extraEntries.every(([key, value]) => entry && entry[key] === value);
+  const isPlainObject = (entry) =>
+    typeof entry === "object" && entry != null && !Array.isArray(entry);
+  const normalizeManagedServerName = (value) =>
+    typeof value === "string" ? value.trim().toLowerCase() : null;
+  const collectDocdexSectionEntry = (section) => {
+    if (!isPlainObject(section)) return {};
+    for (const [key, value] of Object.entries(section)) {
+      if (normalizeManagedServerName(key) === "docdex" && isPlainObject(value)) {
+        return { ...value };
+      }
+    }
+    return {};
+  };
+  const removeDocdexFromSection = (key) => {
+    const section = root[key];
+    if (Array.isArray(section)) {
+      const filtered = section.filter(
+        (entry) => normalizeManagedServerName(entry?.name) !== "docdex"
+      );
+      if (filtered.length !== section.length) {
+        root[key] = filtered;
+      }
+      return;
+    }
+    if (!isPlainObject(section)) {
+      return;
+    }
+    let removed = false;
+    for (const configKey of Object.keys(section)) {
+      if (normalizeManagedServerName(configKey) === "docdex") {
+        delete section[configKey];
+        removed = true;
+      }
+    }
+    if (removed && Object.keys(section).length === 0) {
+      delete root[key];
+    }
+  };
   const pickSection = () => {
     if (root.mcpServers && typeof root.mcpServers === "object" && !Array.isArray(root.mcpServers)) {
       return { key: "mcpServers", section: root.mcpServers };
@@ -1103,29 +1148,42 @@ function upsertMcpServerJson(pathname, url, options = {}) {
     return null;
   };
   if (Array.isArray(root.mcpServers)) {
-    const idx = root.mcpServers.findIndex((entry) => entry && entry.name === "docdex");
-    if (idx >= 0) {
-      const current = root.mcpServers[idx] || {};
-      if (current.url === url && matchesExtras(current)) return false;
-      root.mcpServers[idx] = { ...current, ...extra, url, name: "docdex" };
-      writeJson(pathname, root);
-      return true;
+    const nextEntries = [];
+    let insertIndex = -1;
+    let current = {};
+    for (const entry of root.mcpServers) {
+      if (normalizeManagedServerName(entry?.name) === "docdex") {
+        if (insertIndex === -1) {
+          insertIndex = nextEntries.length;
+          current = isPlainObject(entry) ? { ...entry } : {};
+        }
+        continue;
+      }
+      nextEntries.push(entry);
     }
-    root.mcpServers.push({ ...extra, url, name: "docdex" });
-    writeJson(pathname, root);
-    return true;
-  }
-
-  const picked = pickSection();
-  if (!picked) {
-    root.mcpServers = {};
+    const nextEntry = { ...current, ...extra, url, name: "docdex" };
+    if (insertIndex === -1) {
+      nextEntries.push(nextEntry);
+    } else {
+      nextEntries.splice(insertIndex, 0, nextEntry);
+    }
+    root.mcpServers = nextEntries;
+    removeDocdexFromSection("mcp_servers");
+  } else {
+    const picked = pickSection();
+    const sectionKey = picked ? picked.key : "mcpServers";
+    if (!picked) {
+      root[sectionKey] = {};
+    }
+    const current = collectDocdexSectionEntry(root[sectionKey]);
+    removeDocdexFromSection(sectionKey);
+    if (!root[sectionKey] || !isPlainObject(root[sectionKey])) {
+      root[sectionKey] = {};
+    }
+    root[sectionKey].docdex = { ...current, ...extra, url };
+    removeDocdexFromSection(sectionKey === "mcpServers" ? "mcp_servers" : "mcpServers");
   }
-  const section = picked ? picked.section : root.mcpServers;
-  const current = section.docdex;
-  if (current && current.url === url && matchesExtras(current)) return false;
-  const base =
-    current && typeof current === "object" && !Array.isArray(current) ? current : {};
-  section.docdex = { ...base, ...extra, url };
+  if (JSON.stringify(root) === before) return false;
   writeJson(pathname, root);
   return true;
 }
@@ -1137,7 +1195,15 @@ function upsertZedConfig(pathname, url) {
   if (!root.experimental_mcp_servers || typeof root.experimental_mcp_servers !== "object" || Array.isArray(root.experimental_mcp_servers)) {
     root.experimental_mcp_servers = {};
   }
-  const current = root.experimental_mcp_servers.docdex;
+  const normalizeManagedServerName = (value) =>
+    typeof value === "string" ? value.trim().toLowerCase() : null;
+  let current = root.experimental_mcp_servers.docdex;
+  for (const key of Object.keys(root.experimental_mcp_servers)) {
+    if (normalizeManagedServerName(key) === "docdex" && key !== "docdex") {
+      if (current == null) current = root.experimental_mcp_servers[key];
+      delete root.experimental_mcp_servers[key];
+    }
+  }
   if (current && current.url === url) return false;
   root.experimental_mcp_servers.docdex = { url };
   writeJson(pathname, root);
@@ -1146,16 +1212,52 @@ function upsertZedConfig(pathname, url) {
 
 function upsertCodexConfig(pathname, url) {
   const codexTimeoutSec = 300;
-  const hasSection = (contents, section) =>
-    new RegExp(`^\\s*\\[${section}\\]\\s*$`, "m").test(contents);
-  const hasNestedMcpServers = (contents) =>
-    /^\s*\[mcp_servers\.[^\]]+\]\s*$/m.test(contents);
   const legacyInstructionPath = "~/.docdex/agents.md";
   const parseTomlString = (value) => {
     const trimmed = value.trim();
     const quoted = trimmed.match(/^"(.*)"$/) || trimmed.match(/^'(.*)'$/);
     return quoted ? quoted[1] : trimmed;
   };
+  const normalizeTomlKeyPart = (value) => parseTomlString(value).trim();
+  const parseTomlHeaderParts = (line) => {
+    const match = line.match(/^\s*\[([^\]]+)\]\s*$/);
+    if (!match) return null;
+    return match[1].split(".").map(normalizeTomlKeyPart).filter((part) => part.length > 0);
+  };
+  const hasSection = (contents, section) => {
+    const expectedParts = section.split(".").map(normalizeTomlKeyPart);
+    return contents
+      .split(/\r?\n/)
+      .some((line) => {
+        const parts = parseTomlHeaderParts(line);
+        return (
+          parts &&
+          parts.length === expectedParts.length &&
+          parts.every((part, index) => part === expectedParts[index])
+        );
+      });
+  };
+  const isTomlSectionLine = (line) => parseTomlHeaderParts(line) != null;
+  const isMcpServersSectionLine = (line) => {
+    const parts = parseTomlHeaderParts(line);
+    return !!parts && parts.length === 1 && parts[0] === "mcp_servers";
+  };
+  const isDocdexNestedMcpServerSectionLine = (line) => {
+    const parts = parseTomlHeaderParts(line);
+    return !!parts && parts.length === 2 && parts[0] === "mcp_servers" && parts[1] === "docdex";
+  };
+  const hasNestedMcpServers = (contents) =>
+    contents
+      .split(/\r?\n/)
+      .some((line) => {
+        const parts = parseTomlHeaderParts(line);
+        return !!parts && parts.length > 1 && parts[0] === "mcp_servers";
+      });
+  const parseTomlAssignmentKey = (line) => {
+    const match = line.match(/^\s*([^=]+?)\s*=/);
+    return match ? normalizeTomlKeyPart(match[1]) : null;
+  };
+  const isDocdexAssignmentLine = (line) => parseTomlAssignmentKey(line) === "docdex";
   const migrateLegacyMcpServers = (contents) => {
     if (!/\[\[mcp_servers\]\]/m.test(contents)) {
       return { contents, migrated: false };
@@ -1220,8 +1322,7 @@ function upsertCodexConfig(pathname, url) {
       ["startup_timeout_sec", `${codexTimeoutSec}`]
     ];
     const lines = contents.split(/\r?\n/);
-    const headerRe = /^\s*\[mcp_servers\.docdex\]\s*$/;
-    let start = lines.findIndex((line) => headerRe.test(line));
+    let start = lines.findIndex((line) => isDocdexNestedMcpServerSectionLine(line));
     if (start === -1) {
       if (lines.length && lines[lines.length - 1].trim()) lines.push("");
       lines.push("[mcp_servers.docdex]");
@@ -1231,7 +1332,7 @@ function upsertCodexConfig(pathname, url) {
       return { contents: lines.join("\n"), updated: true };
     }
     let end = start + 1;
-    while (end < lines.length && !/^\s*\[.+\]\s*$/.test(lines[end])) {
+    while (end < lines.length && !isTomlSectionLine(lines[end])) {
       end += 1;
     }
     let updated = false;
@@ -1239,7 +1340,7 @@ function upsertCodexConfig(pathname, url) {
       const lineValue = `${key} = ${value}`;
       let keyIndex = -1;
       for (let i = start + 1; i < end; i += 1) {
-        if (new RegExp(`^\\s*${key}\\s*=`).test(lines[i])) {
+        if (parseTomlAssignmentKey(lines[i]) === key) {
           keyIndex = i;
           break;
         }
@@ -1260,8 +1361,7 @@ function upsertCodexConfig(pathname, url) {
     const entryLine =
       `docdex = { url = "${urlValue}", tool_timeout_sec = ${codexTimeoutSec}, startup_timeout_sec = ${codexTimeoutSec} }`;
     const lines = contents.split(/\r?\n/);
-    const headerRe = /^\s*\[mcp_servers\]\s*$/;
-    const start = lines.findIndex((line) => headerRe.test(line));
+    const start = lines.findIndex((line) => isMcpServersSectionLine(line));
     if (start === -1) {
       if (lines.length && lines[lines.length - 1].trim()) lines.push("");
       lines.push("[mcp_servers]");
@@ -1269,23 +1369,29 @@ function upsertCodexConfig(pathname, url) {
       return { contents: lines.join("\n"), updated: true };
     }
     let end = start + 1;
-    while (end < lines.length && !/^\s*\[.+\]\s*$/.test(lines[end])) {
+    while (end < lines.length && !isTomlSectionLine(lines[end])) {
       end += 1;
     }
     let updated = false;
-    let docdexLine = -1;
+    const docdexLines = [];
     for (let i = start + 1; i < end; i += 1) {
-      if (/^\s*docdex\s*=/.test(lines[i])) {
-        docdexLine = i;
-        break;
+      if (isDocdexAssignmentLine(lines[i])) {
+        docdexLines.push(i);
       }
     }
-    if (docdexLine === -1) {
+    if (docdexLines.length === 0) {
       lines.splice(end, 0, entryLine);
       updated = true;
-    } else if (lines[docdexLine].trim() !== entryLine) {
-      lines[docdexLine] = entryLine;
-      updated = true;
+    } else {
+      const [firstDocdexLine, ...extraDocdexLines] = docdexLines;
+      if (lines[firstDocdexLine].trim() !== entryLine) {
+        lines[firstDocdexLine] = entryLine;
+        updated = true;
+      }
+      for (let i = extraDocdexLines.length - 1; i >= 0; i -= 1) {
+        lines.splice(extraDocdexLines[i], 1);
+        updated = true;
+      }
     }
     return { contents: lines.join("\n"), updated };
   };
@@ -1307,10 +1413,10 @@ function upsertCodexConfig(pathname, url) {
     };
 
     for (const line of lines) {
-      const section = line.match(/^\s*\[([^\]]+)\]\s*$/);
+      const section = parseTomlHeaderParts(line);
       if (section) {
         flushFeatures();
-        if (section[1].trim() === "features") {
+        if (section.length === 1 && section[0] === "features") {
           inFeatures = true;
           buffer = [line];
           continue;
@@ -1336,6 +1442,73 @@ function upsertCodexConfig(pathname, url) {
     return { contents: output.join("\n"), updated };
   };
 
+  const removeRootDocdexEntries = (text) => {
+    const lines = text.split(/\r?\n/);
+    const output = [];
+    let inRootSection = false;
+    let updated = false;
+    for (const line of lines) {
+      const section = parseTomlHeaderParts(line);
+      if (section) {
+        inRootSection = section.length === 1 && section[0] === "mcp_servers";
+        output.push(line);
+        continue;
+      }
+      if (inRootSection && isDocdexAssignmentLine(line)) {
+        updated = true;
+        continue;
+      }
+      output.push(line);
+    }
+    return { contents: output.join("\n"), updated };
+  };
+
+  const countRootDocdexEntries = (text) => {
+    const lines = text.split(/\r?\n/);
+    let inRootSection = false;
+    let count = 0;
+    for (const line of lines) {
+      const section = parseTomlHeaderParts(line);
+      if (section) {
+        inRootSection = section.length === 1 && section[0] === "mcp_servers";
+        continue;
+      }
+      if (inRootSection && isDocdexAssignmentLine(line)) {
+        count += 1;
+      }
+    }
+    return count;
+  };
+
+  const removeNestedDocdexSections = (text) => {
+    const lines = text.split(/\r?\n/);
+    const output = [];
+    let skipping = false;
+    let updated = false;
+    for (const line of lines) {
+      const isSection = isTomlSectionLine(line);
+      if (skipping) {
+        if (isSection) {
+          skipping = false;
+        } else {
+          continue;
+        }
+      }
+      if (isDocdexNestedMcpServerSectionLine(line)) {
+        skipping = true;
+        updated = true;
+        continue;
+      }
+      output.push(line);
+    }
+    return { contents: output.join("\n"), updated };
+  };
+
+  const countNestedDocdexSections = (text) =>
+    text
+      .split(/\r?\n/)
+      .filter((line) => isDocdexNestedMcpServerSectionLine(line)).length;
+
   let contents = "";
   if (fs.existsSync(pathname)) {
     contents = fs.readFileSync(pathname, "utf8");
@@ -1351,7 +1524,23 @@ function upsertCodexConfig(pathname, url) {
   contents = cleaned.contents;
   updated = updated || cleaned.updated;
 
-  if (hasNestedMcpServers(contents)) {
+  const preferNested = hasNestedMcpServers(contents);
+  const rootDocdexCount = countRootDocdexEntries(contents);
+  const nestedDocdexCount = countNestedDocdexSections(contents);
+
+  if (preferNested && rootDocdexCount > 0) {
+    const prunedRoot = removeRootDocdexEntries(contents);
+    contents = prunedRoot.contents;
+    updated = updated || prunedRoot.updated;
+  }
+
+  if ((!preferNested && nestedDocdexCount > 0) || (preferNested && nestedDocdexCount > 1)) {
+    const prunedNested = removeNestedDocdexSections(contents);
+    contents = prunedNested.contents;
+    updated = updated || prunedNested.updated;
+  }
+
+  if (preferNested) {
     const nested = upsertDocdexNested(contents, url);
     contents = nested.contents;
     updated = updated || nested.updated;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "docdex",
-  "version": "0.2.59",
+  "version": "0.2.61",
   "mcpName": "io.github.bekirdag/docdex",
   "description": "Local-first documentation and code indexer with HTTP/MCP search, AST, and agent memory.",
   "bin": {