claude-memory-admin 1.9.0 → 1.10.0

package/server.mjs

@@ -12,6 +12,8 @@ import { projectsRoot, resolveRoot } from './src/projects.mjs';
 import { buildStore } from './src/model.mjs';
 import { resolveGlobalInstructions, resolveInstructions, summarise } from './src/instructions.mjs';
 import { settingsReport, summariseSettings } from './src/settings.mjs';
+import { costReport, writeUserSetting } from './src/cost.mjs';
+import { AGENTS_DIR, AGENT_FIELDS, agentsDirExists, listAgents, setAgentField } from './src/agents.mjs';
 import { listStores } from './src/stores.mjs';
 import { forgetPath, rememberPath } from './src/pathcache.mjs';
 import { searchAll } from './src/search.mjs';
@@ -147,15 +149,23 @@ function storeProjectDir(store) {
 
 /**
  * The global store holds instructions, not memory, and its directory is ~/.claude
- * itself. Every write endpoint below resolves a target inside `store.dir`, so
- * without this guard a delete aimed at it would land on the user's CLAUDE.md and
- * settings rather than on a memory file. It is read-only, and refused here once
- * rather than in each of the fifteen handlers.
+ * itself. Every memory write endpoint below resolves a target inside `store.dir`,
+ * so without this guard a delete aimed at it would land on the user's CLAUDE.md
+ * and settings rather than on a memory file. It is refused here once rather than
+ * in each of the fifteen handlers.
+ *
+ * The Cost handlers are the two exceptions, and the only writes this app makes
+ * outside a memory store. They do not take a path from the request at all: one
+ * writes an allowlisted key to ~/.claude/settings.json, the other one of two
+ * frontmatter fields in a named file inside ~/.claude/agents. Neither can reach
+ * an instruction file, which is what the rest of this guard exists to protect.
  */
-export function refuseWritesToGlobal(store, method) {
-  if (store.kind === 'global' && method !== 'GET') {
-    throw new Error('The global store is read-only: it holds instruction files, not memory.');
-  }
+const GLOBAL_WRITE_ACTIONS = new Set(['cost/setting', 'cost/agent']);
+
+export function refuseWritesToGlobal(store, method, action = null) {
+  if (store.kind !== 'global' || method === 'GET') return;
+  if (action && GLOBAL_WRITE_ACTIONS.has(action)) return;
+  throw new Error('The global store is read-only: it holds instruction files, not memory.');
 }
 
 /** A store with nothing to build a memory model from, in the shape the frontend expects. */
@@ -260,9 +270,9 @@ async function handleApi(req, res, url) {
   }
 
   const store = requireStore(decodeURIComponent(segments[2]));
-  refuseWritesToGlobal(store, req.method);
-  const dir = store.dir;
   const action = segments.slice(3).join('/');
+  refuseWritesToGlobal(store, req.method, action);
+  const dir = store.dir;
 
   if (!action && req.method === 'GET') {
     // buildStore reads every .md in the directory as a memory file, which for
@@ -312,6 +322,34 @@ async function handleApi(req, res, url) {
     return sendJson(res, 200, settingsReport({ projectDir: storeProjectDir(store) }));
   }
 
+  // The Cost segment. User scope only: the knobs it writes are about every
+  // session on the machine, and the file it writes them to is ~/.claude/settings.json.
+  if ((action === 'cost' || action.startsWith('cost/')) && store.kind !== 'global') {
+    return sendJson(res, 400, { error: 'The cost settings are user-scope, and are edited from the Global entry.' });
+  }
+
+  if (action === 'cost' && req.method === 'GET') {
+    return sendJson(res, 200, {
+      settings: costReport(),
+      agents: listAgents(),
+      agentsDir: AGENTS_DIR,
+      agentsDirExists: agentsDirExists(),
+      agentFields: AGENT_FIELDS,
+    });
+  }
+
+  if (action === 'cost/setting' && req.method === 'POST') {
+    const body = await readBody(req);
+    writeUserSetting(body.key, body.value ?? null);
+    return sendJson(res, 200, { settings: costReport() });
+  }
+
+  if (action === 'cost/agent' && req.method === 'POST') {
+    const body = await readBody(req);
+    const agents = setAgentField(body.file, body.field, body.value ?? null);
+    return sendJson(res, 200, { agents, agentsDir: AGENTS_DIR, agentsDirExists: agentsDirExists() });
+  }
+
   if (action === 'delete-preview' && req.method === 'POST') {
     const body = await readBody(req);
     return sendJson(res, 200, deletePreview(dir, body.file));

package/src/agents.mjs

@@ -0,0 +1,268 @@
+// User-scope subagent definitions: ~/.claude/agents/*.md.
+//
+// Not to be confused with ~/.claude/agent-memory (src/stores.mjs), which is what
+// those agents *remember*. This module is about what they *are*: a markdown file
+// whose frontmatter names the agent and, optionally, pins the model and effort
+// it runs at. Pinning a summariser to Haiku while a reviewer stays on Opus is the
+// finer-grained version of the CLAUDE_CODE_SUBAGENT_MODEL switch in src/cost.mjs,
+// which - worth remembering when both are set - outranks everything here.
+//
+// Only `model` and `effort` are writable. The prompt body, the tool lists and
+// every other field are read and shown but never rewritten: a body is prose
+// somebody wrote on purpose, and this tool has no view on it.
+
+import fs from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+
+import { parseFrontmatter } from './parse.mjs';
+import { writeFileAtomic } from './mutate.mjs';
+
+export const AGENTS_DIR = path.join(os.homedir(), '.claude', 'agents');
+
+const MODEL_ID = /^claude-[A-Za-z0-9._[\]-]+$/;
+
+export const AGENT_FIELDS = {
+  model: {
+    unset: 'inherit',
+    allowModelId: true,
+    options: [
+      { value: null, label: 'inherit', note: 'the session model' },
+      { value: 'haiku', label: 'haiku' },
+      { value: 'sonnet', label: 'sonnet' },
+      { value: 'opus', label: 'opus' },
+      { value: 'fable', label: 'fable' },
+    ],
+  },
+  effort: {
+    unset: 'default',
+    allowModelId: false,
+    options: [
+      { value: null, label: 'default', note: 'the session effort' },
+      { value: 'low', label: 'low' },
+      { value: 'medium', label: 'medium' },
+      { value: 'high', label: 'high' },
+      { value: 'xhigh', label: 'xhigh' },
+      { value: 'max', label: 'max' },
+    ],
+  },
+};
+
+export const AGENT_PROBLEM_SEVERITY = {
+  'no-frontmatter': 'bad',
+  'missing-name': 'warn',
+  'missing-description': 'warn',
+  'name-mismatch': 'warn',
+  'unknown-model': 'warn',
+  'unknown-effort': 'warn',
+};
+
+function known(field, value) {
+  const spec = AGENT_FIELDS[field];
+  if (spec.options.some((option) => option.value === value)) return true;
+  return spec.allowModelId && MODEL_ID.test(value);
+}
+
+/**
+ * A filename this module is willing to touch, resolved inside the agents
+ * directory. The same shape as safeMemoryPath in src/mutate.mjs: a bare .md
+ * basename, no dotfiles, and a realpath check so a symlink cannot point the
+ * write somewhere else.
+ */
+export function safeAgentPath(dir, file) {
+  if (typeof file !== 'string' || !file || file.includes('\0')) {
+    throw new Error('Invalid filename');
+  }
+  if (file !== path.basename(file) || file.startsWith('.') || !file.endsWith('.md')) {
+    throw new Error(`Refusing to touch "${file}": must be a plain .md filename`);
+  }
+
+  const full = path.join(dir, file);
+  const rel = path.relative(dir, full);
+  if (rel.startsWith('..') || path.isAbsolute(rel)) {
+    throw new Error('Path escapes the agents directory');
+  }
+  if (fs.existsSync(full)) {
+    const realDir = fs.realpathSync(dir);
+    const realFull = fs.realpathSync(full);
+    if (path.relative(realDir, realFull).startsWith('..')) {
+      throw new Error('Path escapes the agents directory');
+    }
+  }
+  return full;
+}
+
+function describeAgent(dir, file) {
+  const full = path.join(dir, file);
+  const stem = file.replace(/\.md$/, '');
+
+  let text;
+  try {
+    text = fs.readFileSync(full, 'utf8');
+  } catch (err) {
+    return {
+      file,
+      name: stem,
+      description: '',
+      tools: '',
+      model: null,
+      effort: null,
+      bytes: 0,
+      problems: [{ kind: 'no-frontmatter', severity: 'bad', detail: err.message }],
+    };
+  }
+
+  const { data, hasFrontmatter } = parseFrontmatter(text);
+  const scalar = (key) => (typeof data[key] === 'string' ? data[key].trim() : '');
+  const name = scalar('name') || stem;
+  const model = scalar('model') || null;
+  const effort = scalar('effort') || null;
+
+  const problems = [];
+  const flag = (kind, detail) => problems.push({ kind, severity: AGENT_PROBLEM_SEVERITY[kind], detail });
+
+  if (!hasFrontmatter) {
+    flag('no-frontmatter', 'The file has no --- frontmatter block, so Claude Code does not read it as an agent definition.');
+  } else {
+    if (!scalar('name')) flag('missing-name', `No name: field, so the agent is addressed as "${stem}" after its file.`);
+    if (!scalar('description')) flag('missing-description', 'No description: field. Claude decides when to delegate from that description, so an agent without one is never chosen on its own.');
+    if (scalar('name') && scalar('name') !== stem) flag('name-mismatch', `Named "${scalar('name')}" in a file called "${file}".`);
+    if (model && !known('model', model)) flag('unknown-model', `model: ${model} is neither an alias nor a claude- model name.`);
+    if (effort && !known('effort', effort)) flag('unknown-effort', `effort: ${effort} is not one of low, medium, high, xhigh or max.`);
+  }
+
+  return {
+    file,
+    name,
+    description: scalar('description'),
+    tools: scalar('tools'),
+    model,
+    effort,
+    bytes: Buffer.byteLength(text, 'utf8'),
+    problems,
+  };
+}
+
+/**
+ * Every user-scope agent definition. A directory that is not there is the
+ * ordinary state of a machine whose owner has never written one, not a failure,
+ * so it answers with an empty list.
+ */
+export function listAgents({ dir = AGENTS_DIR } = {}) {
+  let entries;
+  try {
+    entries = fs.readdirSync(dir, { withFileTypes: true });
+  } catch {
+    return [];
+  }
+
+  return entries
+    .filter((entry) => entry.isFile() && entry.name.endsWith('.md') && !entry.name.startsWith('.'))
+    .map((entry) => describeAgent(dir, entry.name))
+    .sort((a, b) => a.name.localeCompare(b.name));
+}
+
+/** Whether the directory itself exists, which is what tells an empty list from a missing one. */
+export function agentsDirExists({ dir = AGENTS_DIR } = {}) {
+  try {
+    return fs.statSync(dir).isDirectory();
+  } catch {
+    return false;
+  }
+}
+
+const fieldLine = (field) => new RegExp(`^${field}[ \\t]*:`);
+
+/**
+ * Where a field that is not there yet should go: straight after the name or
+ * description when that line carries its value inline, and otherwise at the end
+ * of the block. Appending is always valid - a top-level key ends whatever nested
+ * block preceded it - so the nicer placement is only taken when it is provably
+ * safe, which rules out a folded or block scalar the insertion would land inside.
+ */
+function inlineScalarAt(block, key) {
+  const index = block.findIndex((line) => fieldLine(key).test(line));
+  if (index === -1) return -1;
+  const rest = block[index].slice(block[index].indexOf(':') + 1).trim();
+  if (!rest || rest.startsWith('|') || rest.startsWith('>')) return -1;
+  return index;
+}
+
+function insertionIndex(block) {
+  const description = block.findIndex((line) => fieldLine('description').test(line));
+  const inline = inlineScalarAt(block, 'description');
+  if (inline !== -1) return inline + 1;
+  if (description !== -1) return block.length;
+
+  const name = inlineScalarAt(block, 'name');
+  return name === -1 ? block.length : name + 1;
+}
+
+/**
+ * Rewrite one frontmatter field, leaving every other byte of the file alone:
+ * the body, the other fields, their order, their spacing and any comments among
+ * them. The same principle src/parse.mjs applies to MEMORY.md - edit the line
+ * that changed, never re-emit the document from a parse of it.
+ */
+export function rewriteAgentField(text, field, value) {
+  const lines = text.split('\n');
+  if (lines[0]?.trim() !== '---') {
+    throw new Error('This file has no frontmatter block, so there is nothing to set.');
+  }
+
+  let end = -1;
+  for (let i = 1; i < lines.length; i++) {
+    if (lines[i].trim() === '---') { end = i; break; }
+  }
+  if (end === -1) {
+    throw new Error('This file has an unterminated frontmatter block.');
+  }
+
+  const block = lines.slice(1, end);
+  const at = block.findIndex((line) => fieldLine(field).test(line));
+
+  if (value === null) {
+    if (at === -1) return text;
+    block.splice(at, 1);
+  } else if (at === -1) {
+    block.splice(insertionIndex(block), 0, `${field}: ${value}`);
+  } else {
+    block[at] = `${field}: ${value}`;
+  }
+
+  return [lines[0], ...block, ...lines.slice(end)].join('\n');
+}
+
+function normaliseAgentValue(field, value) {
+  const spec = AGENT_FIELDS[field];
+  if (value === null || value === undefined) return null;
+  if (typeof value !== 'string') throw new Error(`${field} takes a string, not ${typeof value}.`);
+
+  const trimmed = value.trim();
+  if (!trimmed || trimmed === spec.unset) return null;
+  if (known(field, trimmed)) return trimmed;
+
+  throw new Error(`"${trimmed}" is not a value ${field} accepts.`);
+}
+
+/**
+ * Set or clear `model` or `effort` on one agent file, atomically, and answer with
+ * the refreshed list so the caller renders what is on disk rather than what it
+ * hoped it wrote.
+ */
+export function setAgentField(file, field, value, { dir = AGENTS_DIR } = {}) {
+  if (!Object.prototype.hasOwnProperty.call(AGENT_FIELDS, field)) {
+    throw new Error(`"${field}" is not a field this tool writes. Only model and effort are editable here.`);
+  }
+
+  const full = safeAgentPath(dir, file);
+  if (!fs.existsSync(full)) throw new Error(`${file} is no longer there - reload and try again.`);
+
+  const next = normaliseAgentValue(field, value);
+  const original = fs.readFileSync(full, 'utf8');
+  const rewritten = rewriteAgentField(original, field, next);
+
+  if (rewritten !== original) writeFileAtomic(dir, file, rewritten);
+
+  return listAgents({ dir });
+}

package/src/cost.mjs

@@ -0,0 +1,277 @@
+// The two settings keys that decide what a session costs, and the only two keys
+// this tool ever writes.
+//
+// Everything else in the app reports; this module changes ~/.claude/settings.json.
+// That is a deliberate exception, so the surface is kept as narrow as it can be:
+// a closed list of keys, a closed list of values per key, the user scope only,
+// and a hard refusal to rewrite a settings file that did not parse - overwriting
+// one would silently drop every setting this tool could not read.
+//
+// The two keys:
+//
+//   env.CLAUDE_CODE_SUBAGENT_MODEL  the model every subagent, agent-team member
+//                                   and workflow agent runs on. It outranks both
+//                                   the model asked for at the call site and the
+//                                   `model:` line in an agent file.
+//   outputStyle                     how Claude writes back in the main
+//                                   conversation. Subagents run their own system
+//                                   prompt and are untouched by it.
+
+import fs from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+
+import { parseFrontmatter } from './parse.mjs';
+import { writeFileAtomic } from './mutate.mjs';
+import {
+  SETTINGS_SEVERITY,
+  USER_SETTINGS,
+  readJsonDetailed,
+  readPath,
+  settingsCandidates,
+} from './settings.mjs';
+
+export const OUTPUT_STYLES_DIR = path.join(os.homedir(), '.claude', 'output-styles');
+
+// A full model name is documented as acceptable wherever an alias is, and this
+// tool has no business deciding which ones exist. The shape is checked so a
+// typo does not land in a settings file unnoticed; the value is not resolved.
+const MODEL_ID = /^claude-[A-Za-z0-9._[\]-]+$/;
+
+export const COST_KEYS = [
+  {
+    key: 'subagentModel',
+    path: ['env', 'CLAUDE_CODE_SUBAGENT_MODEL'],
+    label: 'CLAUDE_CODE_SUBAGENT_MODEL',
+    title: 'Subagent model',
+    detail: 'The model every subagent, agent-team member and workflow agent runs on. It overrides the model asked for at the call site and the model: line in an agent file both, so it is the one switch that moves all of them at once. Search and summary work rarely needs more than Haiku.',
+    envVar: 'CLAUDE_CODE_SUBAGENT_MODEL',
+    unset: 'inherit',
+    allowModelId: true,
+    custom: null,
+    options: [
+      { value: null, label: 'inherit', note: 'unset - each agent resolves its own model' },
+      { value: 'haiku', label: 'haiku', note: 'cheapest' },
+      { value: 'sonnet', label: 'sonnet' },
+      { value: 'opus', label: 'opus' },
+      { value: 'fable', label: 'fable', note: 'dearest' },
+    ],
+  },
+  {
+    key: 'outputStyle',
+    path: ['outputStyle'],
+    label: 'outputStyle',
+    title: 'Output style',
+    detail: 'How Claude writes back. Concise leads with the result and drops the narration, which cuts output tokens on every turn; Explanatory and Learning add to them by design. This is part of the system prompt, so a change lands on /clear or the next session, and it reaches the main conversation only.',
+    envVar: null,
+    unset: 'Default',
+    allowModelId: false,
+    custom: 'outputStyles',
+    options: [
+      { value: null, label: 'Default', note: 'unset' },
+      { value: 'Concise', label: 'Concise', note: 'fewest output tokens' },
+      { value: 'Proactive', label: 'Proactive' },
+      { value: 'Explanatory', label: 'Explanatory', note: 'longer answers' },
+      { value: 'Learning', label: 'Learning', note: 'longer answers' },
+    ],
+  },
+];
+
+/**
+ * Custom output styles in the user scope. The file name is the style name unless
+ * the frontmatter overrides it, which is the rule Claude Code applies, and a
+ * directory that is not there is the normal case rather than a failure.
+ */
+export function listOutputStyles({ dir = OUTPUT_STYLES_DIR } = {}) {
+  let entries;
+  try {
+    entries = fs.readdirSync(dir, { withFileTypes: true });
+  } catch {
+    return [];
+  }
+
+  return entries
+    .filter((entry) => entry.isFile() && entry.name.endsWith('.md'))
+    .map((entry) => {
+      const file = path.join(dir, entry.name);
+      let named = '';
+      try {
+        named = String(parseFrontmatter(fs.readFileSync(file, 'utf8')).data.name || '').trim();
+      } catch { /* an unreadable style still has a name: its file */ }
+      return { name: named || entry.name.replace(/\.md$/, ''), file };
+    })
+    .sort((a, b) => a.name.localeCompare(b.name));
+}
+
+/** The descriptor's own options, plus any custom output styles found on disk. */
+function optionsFor(descriptor, outputStyles) {
+  const options = descriptor.options.map((option) => ({ ...option }));
+  if (descriptor.custom === 'outputStyles') {
+    for (const style of outputStyles) {
+      if (!options.some((option) => option.value === style.name)) {
+        options.push({ value: style.name, label: style.name, note: 'custom' });
+      }
+    }
+  }
+  return options;
+}
+
+/**
+ * What a value means once it is checked: a string to write, or null to remove
+ * the key. Anything the key does not accept throws rather than being coerced,
+ * because a coerced value would be written to the user's settings file.
+ */
+export function normaliseCostValue(descriptor, value, outputStyles = []) {
+  if (value === null || value === undefined) return null;
+  if (typeof value !== 'string') {
+    throw new Error(`${descriptor.label} takes a string, not ${Array.isArray(value) ? 'a list' : typeof value}.`);
+  }
+
+  const trimmed = value.trim();
+  if (!trimmed || trimmed === descriptor.unset) return null;
+
+  const allowed = optionsFor(descriptor, outputStyles)
+    .map((option) => option.value)
+    .filter((option) => option !== null);
+  if (allowed.includes(trimmed)) return trimmed;
+  if (descriptor.allowModelId && MODEL_ID.test(trimmed)) return trimmed;
+
+  throw new Error(`"${trimmed}" is not a value ${descriptor.label} accepts.`);
+}
+
+/**
+ * Set or remove a nested key, pruning a parent object the removal emptied. A
+ * leftover `"env": {}` is harmless but reads as a setting that is still there,
+ * which is exactly the confusion this panel exists to remove.
+ */
+function setPath(data, keyPath, value) {
+  const [head, ...rest] = keyPath;
+
+  if (!rest.length) {
+    if (value === null) delete data[head];
+    else data[head] = value;
+    return;
+  }
+
+  const child = data[head];
+  const usable = child && typeof child === 'object' && !Array.isArray(child);
+
+  if (value === null) {
+    if (!usable) return;
+    setPath(child, rest, null);
+    if (!Object.keys(child).length) delete data[head];
+    return;
+  }
+
+  if (!usable) data[head] = {};
+  setPath(data[head], rest, value);
+}
+
+/**
+ * Every layer's value for both keys, strongest first, in the same shape the
+ * Settings report uses so the two render identically.
+ *
+ * `shadowedByStronger` is the one thing this adds: the user file is the weakest
+ * of the five, so a value set anywhere else means a write here changes nothing.
+ * Saying so beforehand is cheaper than letting someone watch a setting not take.
+ */
+export function costReport(options = {}) {
+  const {
+    styleDir = OUTPUT_STYLES_DIR,
+    env = process.env,
+    userFile = USER_SETTINGS,
+    ...target
+  } = options;
+
+  const reads = settingsCandidates({ ...target, userFile }).map((candidate) => ({
+    ...candidate,
+    ...readJsonDetailed(candidate.file),
+  }));
+  const layers = reads.map(({ scope, file, status, error }) => ({ scope, file, status, error }));
+  const outputStyles = listOutputStyles({ dir: styleDir });
+
+  const keys = COST_KEYS.map((descriptor) => {
+    const values = reads
+      .filter((read) => read.status === 'ok' && readPath(read.data, descriptor.path) !== undefined)
+      .map((read) => ({
+        scope: read.scope,
+        file: read.file,
+        value: readPath(read.data, descriptor.path),
+        wins: false,
+      }));
+    if (values.length) values[0].wins = true;
+    const winner = values[0] || null;
+
+    const choices = optionsFor(descriptor, outputStyles);
+    // A value the picker cannot offer would be silently replaced the moment
+    // anyone touched the control, so it is pinned into the list instead.
+    if (winner && typeof winner.value === 'string' && winner.value.trim()
+        && !choices.some((option) => option.value === winner.value)) {
+      choices.push({ value: winner.value, label: winner.value, note: 'set in your settings' });
+    }
+
+    const envValue = descriptor.envVar ? env[descriptor.envVar] ?? null : null;
+
+    return {
+      key: descriptor.key,
+      label: descriptor.label,
+      title: descriptor.title,
+      detail: descriptor.detail,
+      unset: descriptor.unset,
+      options: choices,
+      values,
+      effective: winner ? { value: winner.value, scope: winner.scope, file: winner.file } : null,
+      shadowedByStronger: Boolean(winner && winner.scope !== 'user'),
+      envVar: descriptor.envVar,
+      envValue,
+    };
+  });
+
+  const userRead = reads.find((read) => read.file === userFile);
+  const problems = layers
+    .filter((layer) => layer.status !== 'ok' && layer.status !== 'absent')
+    .map((layer) => ({
+      kind: layer.status,
+      severity: SETTINGS_SEVERITY[layer.status] || 'warn',
+      scope: layer.scope,
+      file: layer.file,
+      detail: layer.error,
+    }));
+
+  return {
+    keys,
+    layers,
+    problems,
+    outputStyles,
+    userFile,
+    // False when the file this panel would write is there but unusable. The
+    // controls are disabled rather than allowed to fail on save.
+    writable: !userRead || userRead.status === 'ok' || userRead.status === 'absent',
+  };
+}
+
+/**
+ * Write one key to the user settings file, atomically, and answer with the value
+ * that landed. A file that exists but does not parse is refused outright.
+ */
+export function writeUserSetting(key, value, options = {}) {
+  const { file = USER_SETTINGS, styleDir = OUTPUT_STYLES_DIR } = options;
+
+  const descriptor = COST_KEYS.find((entry) => entry.key === key);
+  if (!descriptor) throw new Error(`"${key}" is not a setting this tool writes.`);
+
+  const next = normaliseCostValue(descriptor, value, listOutputStyles({ dir: styleDir }));
+
+  const read = readJsonDetailed(file);
+  if (read.status !== 'ok' && read.status !== 'absent') {
+    throw new Error(`Refusing to write ${file}: ${read.error || read.status}. Rewriting a file this tool cannot parse would drop the settings it cannot see, so fix the file by hand first.`);
+  }
+
+  const data = read.status === 'ok' ? read.data : {};
+  setPath(data, descriptor.path, next);
+
+  fs.mkdirSync(path.dirname(file), { recursive: true });
+  writeFileAtomic(path.dirname(file), path.basename(file), `${JSON.stringify(data, null, 2)}\n`);
+
+  return next;
+}

package/src/mutate.mjs

@@ -78,11 +78,15 @@ function readIndex(dir) {
 }
 
 /**
- * Replace MEMORY.md atomically: write a sibling temp file, fsync it, rename over
+ * Replace a file atomically: write a sibling temp file, fsync it, rename over
  * the target. A .backup copy is kept for the duration and restored if anything
- * throws, so a crash can never leave a truncated index.
+ * throws, so a crash can never leave a truncated file behind.
+ *
+ * Exported because the settings and agent writers outside this module need the
+ * same guarantee, and a second implementation of it is a second chance to get
+ * the crash path wrong.
  */
-function writeFileAtomic(dir, name, text) {
+export function writeFileAtomic(dir, name, text) {
   const target = path.join(dir, name);
   const tmp = path.join(dir, `.${name}.tmp-${process.pid}`);
   const backup = path.join(dir, `.${name}.backup`);