@gethmy/mcp 3.8.0 → 3.9.0

package/dist/index.js

@@ -18,8 +18,9 @@ var __esm = (fn, res) => () => (fn && (res = fn(fn = 0)), res);
 var __require = /* @__PURE__ */ createRequire(import.meta.url);
 
 // src/config.ts
+import { execFileSync } from "node:child_process";
 import { existsSync as existsSync2, mkdirSync as mkdirSync2, readFileSync as readFileSync2, writeFileSync as writeFileSync2 } from "node:fs";
-import { homedir } from "node:os";
+import { homedir, tmpdir } from "node:os";
 import { dirname, join as join2, parse, resolve } from "node:path";
 function noteLegacyConfigDir(path) {
   if (warnedLegacyConfigDir)
@@ -36,6 +37,23 @@ function noteLegacyLocalPin(path) {
 function noteLocalPinRename(from, to) {
   console.error(`Harmony: wrote the repo pin to ${to} (the pre-#1082 ${from} is now ignored and can be deleted).`);
 }
+function noteUntrackedLocalPin(path) {
+  if (warnedUntrackedLocalPin)
+    return;
+  warnedUntrackedLocalPin = true;
+  console.error(`Harmony: ${path} is ignored by git, so it will not travel with a branch — ` + `a fresh clone, and every worktree the agent daemon cuts, will not have it. ` + `Commit it if you want it to describe this repo everywhere.`);
+}
+function isGitIgnored(path) {
+  try {
+    execFileSync("git", ["check-ignore", "--quiet", path], {
+      cwd: dirname(path),
+      stdio: "ignore"
+    });
+    return true;
+  } catch {
+    return false;
+  }
+}
 function getHmyRootDir() {
   return join2(homedir(), CONFIG_DIR_NAME);
 }
@@ -150,19 +168,96 @@ function saveLocalConfig(config, cwd) {
   if (foundPath !== null && foundPath !== localConfigPath) {
     noteLocalPinRename(foundPath, localConfigPath);
   }
-  const existingConfig = loadLocalConfig(cwd) || {
-    workspaceId: null,
-    projectId: null
-  };
-  const newConfig = { ...existingConfig, ...config };
-  const cleanConfig = {};
-  if (newConfig.workspaceId)
-    cleanConfig.workspaceId = newConfig.workspaceId;
-  if (newConfig.projectId)
-    cleanConfig.projectId = newConfig.projectId;
-  writeFileSync2(localConfigPath, JSON.stringify(cleanConfig, null, 2));
+  const existing = readRawLocalConfig(foundPath ?? localConfigPath);
+  const merged = { ...existing };
+  if ("workspaceId" in config) {
+    if (config.workspaceId)
+      merged.workspaceId = config.workspaceId;
+    else
+      delete merged.workspaceId;
+  }
+  if ("projectId" in config) {
+    if (config.projectId)
+      merged.projectId = config.projectId;
+    else
+      delete merged.projectId;
+  }
+  writeFileSync2(localConfigPath, `${JSON.stringify(merged, null, localIndent(localConfigPath))}
+`);
+  if (isGitIgnored(localConfigPath))
+    noteUntrackedLocalPin(localConfigPath);
   return localConfigPath;
 }
+function readRawLocalConfig(path) {
+  let text;
+  try {
+    text = readFileSync2(path, "utf-8");
+  } catch {
+    return {};
+  }
+  try {
+    const parsed = JSON.parse(text);
+    if (parsed && typeof parsed === "object" && !Array.isArray(parsed)) {
+      return parsed;
+    }
+  } catch {}
+  noteUnparsableLocalPin(path, text);
+  return {};
+}
+function noteUnparsableLocalPin(path, contents) {
+  let backup = null;
+  try {
+    backup = join2(tmpdir(), `hmy-pin-${Date.now()}-${Math.random().toString(36).slice(2, 8)}.json.bak`);
+    writeFileSync2(backup, contents);
+  } catch {
+    backup = null;
+  }
+  console.error(`Harmony: ${path} could not be parsed as JSON, so the pin write REPLACED it. ` + (backup ? `The previous contents are in ${backup}.` : "The previous contents could not be backed up and are gone.") + ` If it carried a "commands" block, re-add it.`);
+}
+function localIndent(configPath) {
+  const root = dirname(configPath);
+  for (const name of ["biome.json", "biome.jsonc"]) {
+    const parsed = readJsonish(join2(root, name));
+    if (!parsed || typeof parsed !== "object")
+      continue;
+    const formatter = parsed.formatter;
+    if (formatter?.indentStyle === "space") {
+      const width = formatter.indentWidth;
+      return typeof width === "number" && width > 0 ? width : 2;
+    }
+    return "\t";
+  }
+  const editorconfig = readTextSafely(join2(root, ".editorconfig"));
+  if (editorconfig) {
+    if (/^\s*indent_style\s*=\s*tab\s*$/im.test(editorconfig))
+      return "\t";
+    const size = editorconfig.match(/^\s*indent_size\s*=\s*(\d+)\s*$/im);
+    if (size) {
+      const width = Number(size[1]);
+      if (width > 0)
+        return width;
+    }
+  }
+  return 2;
+}
+function readJsonish(path) {
+  const text = readTextSafely(path);
+  if (text === null)
+    return null;
+  try {
+    const stripped = text.replace(/^\s*\/\/.*$/gm, "").replace(/,(\s*[}\]])/g, "$1");
+    return JSON.parse(stripped);
+  } catch {
+    return null;
+  }
+}
+function readTextSafely(path) {
+  try {
+    return readFileSync2(path, "utf-8");
+  } catch {
+    return null;
+  }
+}
 function hasLocalConfig(cwd) {
   return findLocalConfigPath(cwd) !== null;
 }
@@ -296,7 +391,7 @@ function getMemoryDir() {
     return config.memoryDir;
   return join2(homedir(), ".harmony", "memory");
 }
-var DEFAULT_API_URL = "https://app.gethmy.com/api", LOCAL_CONFIG_FILENAME = ".hmy.json", LEGACY_LOCAL_CONFIG_FILENAME = ".harmony-mcp.json", CONFIG_DIR_NAME = ".hmy", CONFIG_DIR_SUBDIR = "agent", LEGACY_CONFIG_DIR_NAME = ".harmony-mcp", warnedLegacyConfigDir = false, warnedLegacyLocalPin = false;
+var DEFAULT_API_URL = "https://app.gethmy.com/api", LOCAL_CONFIG_FILENAME = ".hmy.json", LEGACY_LOCAL_CONFIG_FILENAME = ".harmony-mcp.json", CONFIG_DIR_NAME = ".hmy", CONFIG_DIR_SUBDIR = "agent", LEGACY_CONFIG_DIR_NAME = ".harmony-mcp", warnedLegacyConfigDir = false, warnedLegacyLocalPin = false, warnedUntrackedLocalPin = false;
 var init_config = () => {};
 
 // src/prompt-builder.ts
@@ -726,7 +821,7 @@ var init_prompt_builder = __esm(() => {
   };
   VARIANT_INSTRUCTIONS = {
     analysis: `ANALYSIS MODE: Analyze this task thoroughly. Identify requirements, constraints, edge cases, and potential challenges. Do NOT implement anything yet - focus on understanding and planning.`,
-    draft: `DRAFT MODE: Create a detailed implementation plan with code structure, key decisions, and approach. Include pseudocode or skeleton code where helpful. This is for review before full implementation.`,
+    draft: `DRAFT MODE: Draft the approach for review before implementing. Cover the key decisions with their reasons, the data model and the API contracts, and success criteria a test can check. A short signature or schema sketch is fine wherever an interpretation gap would otherwise remain; function bodies, control flow and test code are not - an implementer transcribes a plan faithfully, defects included.`,
     execute: `EXECUTE MODE: Implement this task completely. Write production-ready code following best practices. Include necessary tests and documentation.`
   };
 });
@@ -1037,7 +1132,7 @@ __export(exports_run_state, {
   RUN_STATE_DIR_ENV: () => RUN_STATE_DIR_ENV,
   MAX_POINTER_AGE_MS: () => MAX_POINTER_AGE_MS
 });
-import { execFileSync } from "node:child_process";
+import { execFileSync as execFileSync2 } from "node:child_process";
 import {
   existsSync as existsSync3,
   mkdirSync as mkdirSync3,
@@ -1094,7 +1189,7 @@ function psParentTable() {
     return psTableCache;
   const table = new Map;
   try {
-    const out = execFileSync("ps", ["-Ao", "pid=,ppid="], {
+    const out = execFileSync2("ps", ["-Ao", "pid=,ppid="], {
       encoding: "utf-8",
       timeout: 2000,
       stdio: ["ignore", "pipe", "ignore"]
@@ -4469,81 +4564,6 @@ function parseHmyConfig(text) {
 }
 
 // src/skills.ts
-var HARMONY_WORKFLOW_PROMPT = `# Harmony Card Workflow
-
-Start work on a Harmony card. Card reference: $ARGUMENTS
-
-## 1. Find & Fetch Card
-
-Parse the reference and fetch the card:
-- \`#42\` or \`42\` → \`harmony_get_card\` with \`shortId: 42\`
-- UUID → \`harmony_get_card\` with \`cardId\`
-- Name/text → \`harmony_search_cards\` with \`query\`
-
-## 2. Get Board State
-
-Call \`harmony_get_board\` to get columns and labels. From the response:
-- Find the "In Progress" (or "Progress") column ID
-- Find the "agent" label ID
-
-## 3. Setup Card for Work
-
-Execute these in sequence:
-1. \`harmony_move_card\` → Move to "In Progress" column
-2. \`harmony_add_label_to_card\` → Add "agent" label
-3. \`harmony_start_agent_session\`:
-   - \`cardId\`: Card UUID
-   - \`agentIdentifier\`: Your agent identifier
-   - \`agentName\`: Your agent name
-   - \`currentTask\`: "Analyzing card requirements"
-
-## 4. Generate Work Prompt
-
-Call \`harmony_generate_prompt\` with:
-- \`cardId\` or \`shortId\` (+ \`projectId\` if using shortId)
-- \`variant\`: Select based on task:
-  - \`"execute"\` (default) → Clear tasks, bug fixes, well-defined work
-  - \`"analysis"\` → Complex features, unclear requirements
-  - \`"draft"\` → Medium complexity, want feedback first
-
-The generated prompt provides role framing, focus areas, subtasks, linked cards, and suggested outputs.
-
-## 5. Display Card Summary
-
-Show the user: Card title, short ID, role, priority, labels, due date, description, and subtasks.
-
-## 6. Implement Solution
-
-Work on the card following the generated prompt's guidance. Update progress at milestones:
-- \`harmony_update_agent_progress\` with \`progressPercent\` (0-100), \`currentTask\`, \`status\`, \`blockers\`
-
-**Progress checkpoints:** 20% (exploration), 50% (implementation), 80% (testing), 100% (done)
-
-## 7. Complete Work
-
-When finished:
-1. \`harmony_end_agent_session\` with \`status: "completed"\`, \`progressPercent: 100\`
-2. \`harmony_move_card\` to "Review" column
-3. Summarize accomplishments
-
-If pausing: \`harmony_end_agent_session\` with \`status: "paused"\`
-
-## Key Tools Reference
-
-**Cards:** \`harmony_get_card\` (by \`cardId\`, \`shortId\`, or \`shortIds\`), \`harmony_search_cards\`, \`harmony_create_card\`, \`harmony_update_card\`, \`harmony_move_card\`, \`harmony_delete_card\`, \`harmony_assign_card\`
-
-**Subtasks:** \`harmony_create_subtask\`, \`harmony_toggle_subtask\`, \`harmony_delete_subtask\`
-
-**Labels:** \`harmony_add_label_to_card\`, \`harmony_remove_label_from_card\`, \`harmony_create_label\`
-
-**Links:** \`harmony_add_link_to_card\`, \`harmony_remove_link_from_card\`, \`harmony_get_card_links\`
-
-**Board:** \`harmony_get_board\`, \`harmony_list_projects\`, \`harmony_get_context\`, \`harmony_set_project_context\`
-
-**Sessions:** \`harmony_start_agent_session\`, \`harmony_update_agent_progress\`, \`harmony_end_agent_session\`, \`harmony_get_agent_session\`
-
-**AI:** \`harmony_generate_prompt\`, \`harmony_process_command\`
-`;
 function buildSkillFile(skill) {
   const content = stripSkillPreamble(skill.content);
   if (skill.skillVersion !== undefined && !hasMetadataVersion(content)) {
@@ -6398,7 +6418,7 @@ var TOOLS = {
     }
   },
   harmony_create_plan: {
-    description: "Create a new project plan. Use this to upload implementation plans created during planning. Returns a URL where the plan can be viewed and edited in Harmony.",
+    description: "Create a new project plan. Use this to upload a plan written during planning. Returns a URL where the plan can be viewed and edited in Harmony.",
     inputSchema: {
       type: "object",
       properties: {
@@ -6421,7 +6441,10 @@ var TOOLS = {
           items: {
             type: "object",
             properties: {
-              content: { type: "string", description: "Task description" },
+              content: {
+                type: "string",
+                description: 'One success criterion, as a statement about the finished product that a test can check ("the mirror matches the migration chain"), never a work package ("write the mirror script"). One criterion may take several cards.'
+              },
               priority: {
                 type: "string",
                 enum: ["high", "medium", "low"],
@@ -6435,7 +6458,7 @@ var TOOLS = {
             },
             required: ["content"]
           },
-          description: "Optional list of tasks to create with the plan"
+          description: "The plan's success criteria, one entry each - what must be true when the plan is done, not a breakdown of the work to do it."
         }
       },
       required: ["title"]
@@ -6456,7 +6479,7 @@ var TOOLS = {
     }
   },
   harmony_update_plan: {
-    description: "Update an existing plan. Can update title, content, or status.",
+    description: "Update an existing plan: its title, content, status, or the timeline dates its bar spans. " + "`startDate`/`endDate` are the plan's OWN schedule, the same pair a person sets by dragging the bar in the timeline view. " + "A plan is pinned on both or on neither: send both to schedule it, or both as null to return it to the span derived from its linked cards. " + "Sending one alone is refused unless the plan is already pinned. " + "They are never adjusted automatically — a card running past `endDate` is drawn as an overrun, and only a person extends the plan.",
     inputSchema: {
       type: "object",
       properties: {
@@ -6470,6 +6493,16 @@ var TOOLS = {
           type: "string",
           enum: ["draft", "active", "archived"],
           description: "New status"
+        },
+        startDate: {
+          type: "string",
+          nullable: true,
+          description: "Timeline start as YYYY-MM-DD, or null to unpin (send endDate null too)."
+        },
+        endDate: {
+          type: "string",
+          nullable: true,
+          description: "Timeline end as YYYY-MM-DD, or null to unpin (send startDate null too). Must not precede startDate."
         }
       },
       required: ["planId"]
@@ -8454,6 +8487,13 @@ ${options}
       if (args.status !== undefined) {
         updates.status = z.enum(["draft", "active", "archived"]).parse(args.status);
       }
+      const planDate = z.string().regex(/^\d{4}-\d{2}-\d{2}$/, {
+        message: "expected a date as YYYY-MM-DD"
+      });
+      if (args.startDate !== undefined)
+        updates.startDate = planDate.nullable().parse(args.startDate);
+      if (args.endDate !== undefined)
+        updates.endDate = planDate.nullable().parse(args.endDate);
       const result = await client3.updatePlan(planId, updates);
       return { success: true, plan: result.plan };
     }

package/dist/lib/api-client.js

@@ -15,12 +15,14 @@ var __export = (target, all) => {
 var __esm = (fn, res) => () => (fn && (res = fn(fn = 0)), res);
 
 // src/config.ts
+import { execFileSync } from "node:child_process";
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
-import { homedir } from "node:os";
+import { homedir, tmpdir } from "node:os";
 import { dirname, join, parse, resolve } from "node:path";
 function resetLegacyNoticesForTest() {
   warnedLegacyConfigDir = false;
   warnedLegacyLocalPin = false;
+  warnedUntrackedLocalPin = false;
 }
 function noteLegacyConfigDir(path) {
   if (warnedLegacyConfigDir)
@@ -37,6 +39,23 @@ function noteLegacyLocalPin(path) {
 function noteLocalPinRename(from, to) {
   console.error(`Harmony: wrote the repo pin to ${to} (the pre-#1082 ${from} is now ignored and can be deleted).`);
 }
+function noteUntrackedLocalPin(path) {
+  if (warnedUntrackedLocalPin)
+    return;
+  warnedUntrackedLocalPin = true;
+  console.error(`Harmony: ${path} is ignored by git, so it will not travel with a branch — ` + `a fresh clone, and every worktree the agent daemon cuts, will not have it. ` + `Commit it if you want it to describe this repo everywhere.`);
+}
+function isGitIgnored(path) {
+  try {
+    execFileSync("git", ["check-ignore", "--quiet", path], {
+      cwd: dirname(path),
+      stdio: "ignore"
+    });
+    return true;
+  } catch {
+    return false;
+  }
+}
 function getHmyRootDir() {
   return join(homedir(), CONFIG_DIR_NAME);
 }
@@ -151,19 +170,96 @@ function saveLocalConfig(config, cwd) {
   if (foundPath !== null && foundPath !== localConfigPath) {
     noteLocalPinRename(foundPath, localConfigPath);
   }
-  const existingConfig = loadLocalConfig(cwd) || {
-    workspaceId: null,
-    projectId: null
-  };
-  const newConfig = { ...existingConfig, ...config };
-  const cleanConfig = {};
-  if (newConfig.workspaceId)
-    cleanConfig.workspaceId = newConfig.workspaceId;
-  if (newConfig.projectId)
-    cleanConfig.projectId = newConfig.projectId;
-  writeFileSync(localConfigPath, JSON.stringify(cleanConfig, null, 2));
+  const existing = readRawLocalConfig(foundPath ?? localConfigPath);
+  const merged = { ...existing };
+  if ("workspaceId" in config) {
+    if (config.workspaceId)
+      merged.workspaceId = config.workspaceId;
+    else
+      delete merged.workspaceId;
+  }
+  if ("projectId" in config) {
+    if (config.projectId)
+      merged.projectId = config.projectId;
+    else
+      delete merged.projectId;
+  }
+  writeFileSync(localConfigPath, `${JSON.stringify(merged, null, localIndent(localConfigPath))}
+`);
+  if (isGitIgnored(localConfigPath))
+    noteUntrackedLocalPin(localConfigPath);
   return localConfigPath;
 }
+function readRawLocalConfig(path) {
+  let text;
+  try {
+    text = readFileSync(path, "utf-8");
+  } catch {
+    return {};
+  }
+  try {
+    const parsed = JSON.parse(text);
+    if (parsed && typeof parsed === "object" && !Array.isArray(parsed)) {
+      return parsed;
+    }
+  } catch {}
+  noteUnparsableLocalPin(path, text);
+  return {};
+}
+function noteUnparsableLocalPin(path, contents) {
+  let backup = null;
+  try {
+    backup = join(tmpdir(), `hmy-pin-${Date.now()}-${Math.random().toString(36).slice(2, 8)}.json.bak`);
+    writeFileSync(backup, contents);
+  } catch {
+    backup = null;
+  }
+  console.error(`Harmony: ${path} could not be parsed as JSON, so the pin write REPLACED it. ` + (backup ? `The previous contents are in ${backup}.` : "The previous contents could not be backed up and are gone.") + ` If it carried a "commands" block, re-add it.`);
+}
+function localIndent(configPath) {
+  const root = dirname(configPath);
+  for (const name of ["biome.json", "biome.jsonc"]) {
+    const parsed = readJsonish(join(root, name));
+    if (!parsed || typeof parsed !== "object")
+      continue;
+    const formatter = parsed.formatter;
+    if (formatter?.indentStyle === "space") {
+      const width = formatter.indentWidth;
+      return typeof width === "number" && width > 0 ? width : 2;
+    }
+    return "\t";
+  }
+  const editorconfig = readTextSafely(join(root, ".editorconfig"));
+  if (editorconfig) {
+    if (/^\s*indent_style\s*=\s*tab\s*$/im.test(editorconfig))
+      return "\t";
+    const size = editorconfig.match(/^\s*indent_size\s*=\s*(\d+)\s*$/im);
+    if (size) {
+      const width = Number(size[1]);
+      if (width > 0)
+        return width;
+    }
+  }
+  return 2;
+}
+function readJsonish(path) {
+  const text = readTextSafely(path);
+  if (text === null)
+    return null;
+  try {
+    const stripped = text.replace(/^\s*\/\/.*$/gm, "").replace(/,(\s*[}\]])/g, "$1");
+    return JSON.parse(stripped);
+  } catch {
+    return null;
+  }
+}
+function readTextSafely(path) {
+  try {
+    return readFileSync(path, "utf-8");
+  } catch {
+    return null;
+  }
+}
 function hasLocalConfig(cwd) {
   return findLocalConfigPath(cwd) !== null;
 }
@@ -300,7 +396,7 @@ function getMemoryDir() {
     return config.memoryDir;
   return join(homedir(), ".harmony", "memory");
 }
-var DEFAULT_API_URL = "https://app.gethmy.com/api", LOCAL_CONFIG_FILENAME = ".hmy.json", LEGACY_LOCAL_CONFIG_FILENAME = ".harmony-mcp.json", CONFIG_DIR_NAME = ".hmy", CONFIG_DIR_SUBDIR = "agent", LEGACY_CONFIG_DIR_NAME = ".harmony-mcp", warnedLegacyConfigDir = false, warnedLegacyLocalPin = false;
+var DEFAULT_API_URL = "https://app.gethmy.com/api", LOCAL_CONFIG_FILENAME = ".hmy.json", LEGACY_LOCAL_CONFIG_FILENAME = ".harmony-mcp.json", CONFIG_DIR_NAME = ".hmy", CONFIG_DIR_SUBDIR = "agent", LEGACY_CONFIG_DIR_NAME = ".harmony-mcp", warnedLegacyConfigDir = false, warnedLegacyLocalPin = false, warnedUntrackedLocalPin = false;
 var init_config = () => {};
 
 // src/oauth-login.ts
@@ -864,7 +960,7 @@ var init_prompt_builder = __esm(() => {
   };
   VARIANT_INSTRUCTIONS = {
     analysis: `ANALYSIS MODE: Analyze this task thoroughly. Identify requirements, constraints, edge cases, and potential challenges. Do NOT implement anything yet - focus on understanding and planning.`,
-    draft: `DRAFT MODE: Create a detailed implementation plan with code structure, key decisions, and approach. Include pseudocode or skeleton code where helpful. This is for review before full implementation.`,
+    draft: `DRAFT MODE: Draft the approach for review before implementing. Cover the key decisions with their reasons, the data model and the API contracts, and success criteria a test can check. A short signature or schema sketch is fine wherever an interpretation gap would otherwise remain; function bodies, control flow and test code are not - an implementer transcribes a plan faithfully, defects included.`,
     execute: `EXECUTE MODE: Implement this task completely. Write production-ready code following best practices. Include necessary tests and documentation.`
   };
 });

package/dist/lib/config.js

@@ -15,12 +15,14 @@ var __export = (target, all) => {
 var __esm = (fn, res) => () => (fn && (res = fn(fn = 0)), res);
 
 // src/config.ts
+import { execFileSync } from "node:child_process";
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
-import { homedir } from "node:os";
+import { homedir, tmpdir } from "node:os";
 import { dirname, join, parse, resolve } from "node:path";
 function resetLegacyNoticesForTest() {
   warnedLegacyConfigDir = false;
   warnedLegacyLocalPin = false;
+  warnedUntrackedLocalPin = false;
 }
 function noteLegacyConfigDir(path) {
   if (warnedLegacyConfigDir)
@@ -37,6 +39,23 @@ function noteLegacyLocalPin(path) {
 function noteLocalPinRename(from, to) {
   console.error(`Harmony: wrote the repo pin to ${to} (the pre-#1082 ${from} is now ignored and can be deleted).`);
 }
+function noteUntrackedLocalPin(path) {
+  if (warnedUntrackedLocalPin)
+    return;
+  warnedUntrackedLocalPin = true;
+  console.error(`Harmony: ${path} is ignored by git, so it will not travel with a branch — ` + `a fresh clone, and every worktree the agent daemon cuts, will not have it. ` + `Commit it if you want it to describe this repo everywhere.`);
+}
+function isGitIgnored(path) {
+  try {
+    execFileSync("git", ["check-ignore", "--quiet", path], {
+      cwd: dirname(path),
+      stdio: "ignore"
+    });
+    return true;
+  } catch {
+    return false;
+  }
+}
 function getHmyRootDir() {
   return join(homedir(), CONFIG_DIR_NAME);
 }
@@ -151,19 +170,96 @@ function saveLocalConfig(config, cwd) {
   if (foundPath !== null && foundPath !== localConfigPath) {
     noteLocalPinRename(foundPath, localConfigPath);
   }
-  const existingConfig = loadLocalConfig(cwd) || {
-    workspaceId: null,
-    projectId: null
-  };
-  const newConfig = { ...existingConfig, ...config };
-  const cleanConfig = {};
-  if (newConfig.workspaceId)
-    cleanConfig.workspaceId = newConfig.workspaceId;
-  if (newConfig.projectId)
-    cleanConfig.projectId = newConfig.projectId;
-  writeFileSync(localConfigPath, JSON.stringify(cleanConfig, null, 2));
+  const existing = readRawLocalConfig(foundPath ?? localConfigPath);
+  const merged = { ...existing };
+  if ("workspaceId" in config) {
+    if (config.workspaceId)
+      merged.workspaceId = config.workspaceId;
+    else
+      delete merged.workspaceId;
+  }
+  if ("projectId" in config) {
+    if (config.projectId)
+      merged.projectId = config.projectId;
+    else
+      delete merged.projectId;
+  }
+  writeFileSync(localConfigPath, `${JSON.stringify(merged, null, localIndent(localConfigPath))}
+`);
+  if (isGitIgnored(localConfigPath))
+    noteUntrackedLocalPin(localConfigPath);
   return localConfigPath;
 }
+function readRawLocalConfig(path) {
+  let text;
+  try {
+    text = readFileSync(path, "utf-8");
+  } catch {
+    return {};
+  }
+  try {
+    const parsed = JSON.parse(text);
+    if (parsed && typeof parsed === "object" && !Array.isArray(parsed)) {
+      return parsed;
+    }
+  } catch {}
+  noteUnparsableLocalPin(path, text);
+  return {};
+}
+function noteUnparsableLocalPin(path, contents) {
+  let backup = null;
+  try {
+    backup = join(tmpdir(), `hmy-pin-${Date.now()}-${Math.random().toString(36).slice(2, 8)}.json.bak`);
+    writeFileSync(backup, contents);
+  } catch {
+    backup = null;
+  }
+  console.error(`Harmony: ${path} could not be parsed as JSON, so the pin write REPLACED it. ` + (backup ? `The previous contents are in ${backup}.` : "The previous contents could not be backed up and are gone.") + ` If it carried a "commands" block, re-add it.`);
+}
+function localIndent(configPath) {
+  const root = dirname(configPath);
+  for (const name of ["biome.json", "biome.jsonc"]) {
+    const parsed = readJsonish(join(root, name));
+    if (!parsed || typeof parsed !== "object")
+      continue;
+    const formatter = parsed.formatter;
+    if (formatter?.indentStyle === "space") {
+      const width = formatter.indentWidth;
+      return typeof width === "number" && width > 0 ? width : 2;
+    }
+    return "\t";
+  }
+  const editorconfig = readTextSafely(join(root, ".editorconfig"));
+  if (editorconfig) {
+    if (/^\s*indent_style\s*=\s*tab\s*$/im.test(editorconfig))
+      return "\t";
+    const size = editorconfig.match(/^\s*indent_size\s*=\s*(\d+)\s*$/im);
+    if (size) {
+      const width = Number(size[1]);
+      if (width > 0)
+        return width;
+    }
+  }
+  return 2;
+}
+function readJsonish(path) {
+  const text = readTextSafely(path);
+  if (text === null)
+    return null;
+  try {
+    const stripped = text.replace(/^\s*\/\/.*$/gm, "").replace(/,(\s*[}\]])/g, "$1");
+    return JSON.parse(stripped);
+  } catch {
+    return null;
+  }
+}
+function readTextSafely(path) {
+  try {
+    return readFileSync(path, "utf-8");
+  } catch {
+    return null;
+  }
+}
 function hasLocalConfig(cwd) {
   return findLocalConfigPath(cwd) !== null;
 }
@@ -300,7 +396,7 @@ function getMemoryDir() {
     return config.memoryDir;
   return join(homedir(), ".harmony", "memory");
 }
-var DEFAULT_API_URL = "https://app.gethmy.com/api", LOCAL_CONFIG_FILENAME = ".hmy.json", LEGACY_LOCAL_CONFIG_FILENAME = ".harmony-mcp.json", CONFIG_DIR_NAME = ".hmy", CONFIG_DIR_SUBDIR = "agent", LEGACY_CONFIG_DIR_NAME = ".harmony-mcp", warnedLegacyConfigDir = false, warnedLegacyLocalPin = false;
+var DEFAULT_API_URL = "https://app.gethmy.com/api", LOCAL_CONFIG_FILENAME = ".hmy.json", LEGACY_LOCAL_CONFIG_FILENAME = ".harmony-mcp.json", CONFIG_DIR_NAME = ".hmy", CONFIG_DIR_SUBDIR = "agent", LEGACY_CONFIG_DIR_NAME = ".harmony-mcp", warnedLegacyConfigDir = false, warnedLegacyLocalPin = false, warnedUntrackedLocalPin = false;
 var init_config = () => {};
 init_config();