githits 0.4.10 → 0.4.11

package/dist/cli.js

@@ -62,11 +62,11 @@ import {
   shouldRunUpdateCheck,
   startTelemetrySpan,
   withTelemetrySpan
-} from "./shared/chunk-p9ak72j0.js";
+} from "./shared/chunk-5xd5rcm9.js";
 import {
   __require,
   version
-} from "./shared/chunk-fvpvx4x4.js";
+} from "./shared/chunk-agpezzpd.js";
 
 // src/cli.ts
 import { Command } from "commander";
@@ -3619,9 +3619,9 @@ function isSeverityLabel(value) {
 // src/shared/package-upgrade-review-request.ts
 var DEFAULT_CHANGELOG_LIMIT = 20;
 function buildPackageUpgradeReviewRequest(input) {
-  const batch = input.packages;
-  const hasBatch = batch !== undefined;
-  const hasSingle = input.registry !== undefined || input.packageName !== undefined || input.currentVersion !== undefined || input.targetVersion !== undefined;
+  const batch = input.packages?.filter((pkg) => !isBlankPackageInput(pkg));
+  const hasBatch = Array.isArray(batch) && batch.length > 0;
+  const hasSingle = hasNonBlankValue(input.registry) || hasNonBlankValue(input.packageName) || hasNonBlankValue(input.currentVersion) || hasNonBlankValue(input.targetVersion);
   if (hasBatch && hasSingle) {
     throw new InvalidPackageSpecError("Pass either packages[] or registry/package_name/current_version/target_version, not both.");
   }
@@ -3661,6 +3661,12 @@ function buildUpgradeDependencyProbeParams(pkg, version2, options) {
     includeDependencyChanges: options.includeDependencyChanges
   };
 }
+function hasNonBlankValue(value) {
+  return value !== undefined && value.trim().length > 0;
+}
+function isBlankPackageInput(input) {
+  return !(hasNonBlankValue(input.registry) || hasNonBlankValue(input.packageName) || hasNonBlankValue(input.currentVersion) || hasNonBlankValue(input.targetVersion));
+}
 function parseBatch(packages) {
   if (!Array.isArray(packages) || packages.length === 0) {
     throw new InvalidPackageSpecError("packages[] must contain at least one upgrade.");
@@ -6311,10 +6317,11 @@ function buildUnifiedSearchParams(input) {
   };
 }
 function resolveTargets(target, targets) {
-  if (target && targets) {
+  const nonEmptyTargets = targets?.length ? targets : undefined;
+  if (target && nonEmptyTargets) {
     throw new InvalidArgumentError("Provide either `target` for one search target or `targets` for multiple, not both.");
   }
-  const resolved = target ? [target] : targets ?? [];
+  const resolved = target ? [target] : nonEmptyTargets ?? [];
   if (resolved.length === 0) {
     throw new InvalidArgumentError("Provide either `target` for one search target or `targets` for multiple; neither was set.");
   }
@@ -8076,7 +8083,7 @@ grep run. --symbol-field hydrates enclosing symbol metadata (appears under each
 match in --verbose output; full payload in --json).`;
 function registerCodeGrepCommand(pkgCommand) {
   return pkgCommand.command("grep").summary("Deterministic text grep over indexed dependency source").description(PKG_GREP_DESCRIPTION).argument("[spec-or-pattern]", "Spec mode: package spec (e.g. npm:express). Repo mode (with --repo-url): the pattern.").argument("[pattern-or-prefix]", "Spec mode: the pattern. Repo mode: optional path-prefix.").argument("[path-prefix]", "Spec mode only: optional path-prefix. Ignored with --repo-url.").option("--repo-url <url>", "Repository URL addressing (defaults to the repo default branch)").option("--git-ref <ref>", "Optional tag, commit, branch, or HEAD for --repo-url.").option("--path <path>", "Exact file path to grep").option("--glob <glob>", "Glob scope (repeatable)", collectRepeatable2, []).option("--ext <ext>", "Extension filter without leading dot (repeatable)", collectRepeatable2, []).option("--regex", "Interpret the pattern as RE2 regex").option("--case-sensitive", "Enable ASCII case-sensitive matching").option("-C, --context <n>", "Context lines before and after each match (0-10)").option("-B, --before-context <n>", "Context lines before each match (0-10)").option("-A, --after-context <n>", "Context lines after each match (0-10)").option("--exclude-docs", "Skip files classified as documentation").option("--exclude-tests", "Skip files classified as tests").option("--limit <n>", "Max matches to return on this page (1-1000, default 50)").option("--per-file-limit <n>", "Cap matches per file within this page (0-1000, 0 = unlimited)").option("--cursor <cursor>", "Opaque nextCursor from a previous grep result").option("--symbol-field <field>", `Repeatable; surfaces in --json and under each --verbose match. ${GREP_REPO_SYMBOL_FIELDS_NOTE}`, collectRepeatable2, []).option("--wait <ms>", `Indexing wait timeout (0-${MAX_WAIT_TIMEOUT_MS}, default ${DEFAULT_WAIT_TIMEOUT_MS})`).option("-v, --verbose", "Render grouped output with file headers").option("--json", "Emit the JSON envelope").action(async (arg1, arg2, arg3, options) => {
-    const { createContainer: createContainer2 } = await import("./shared/chunk-mw1910qd.js");
+    const { createContainer: createContainer2 } = await import("./shared/chunk-2w48kb4c.js");
     const deps = await createContainer2();
     await pkgGrepAction(arg1, arg2, arg3, options, {
       codeNavigationService: deps.codeNavigationService,
@@ -9044,7 +9051,7 @@ function registerExampleCommand(program) {
   });
 }
 async function loadContainer() {
-  const { createContainer: createContainer2 } = await import("./shared/chunk-mw1910qd.js");
+  const { createContainer: createContainer2 } = await import("./shared/chunk-2w48kb4c.js");
   return createContainer2();
 }
 // src/commands/feedback.ts
@@ -9117,6 +9124,7 @@ import {
   parse as parseJsonc,
   printParseErrorCode
 } from "jsonc-parser";
+import { parse as parseToml2, stringify as stringifyToml } from "smol-toml";
 import {
   isMap,
   isScalar,
@@ -9199,6 +9207,23 @@ function parseYamlConfigObject(content) {
     };
   }
 }
+function parseTomlConfigObject(content) {
+  const normalizedContent = normalizeConfigContent(content);
+  if (normalizedContent.trim() === "") {
+    return { value: {} };
+  }
+  try {
+    const parsed = parseToml2(normalizedContent);
+    if (!isPlainObject(parsed)) {
+      return { error: "Config file root is not a TOML object" };
+    }
+    return { value: parsed };
+  } catch (err) {
+    return {
+      error: `Invalid TOML: ${err instanceof Error ? err.message : String(err)}`
+    };
+  }
+}
 function formatYamlError(error2) {
   if (error2 instanceof Error) {
     return error2.message;
@@ -9378,6 +9403,9 @@ function parseConfigObjectForFormat(content, format = "json") {
   if (format === "yaml") {
     return parseYamlConfigObject(content);
   }
+  if (format === "toml") {
+    return parseTomlConfigObject(content);
+  }
   const parsed = parseConfigObject(content);
   if (parsed.format === "invalid") {
     return { error: parsed.error };
@@ -9389,11 +9417,24 @@ function renderConfigObjectForFormat(config, format = "json") {
     const rendered = stringifyYaml(config);
     return rendered.endsWith(`
 `) ? rendered : `${rendered}
+`;
+  }
+  if (format === "toml") {
+    const rendered = stringifyToml(config);
+    return rendered.endsWith(`
+`) ? rendered : `${rendered}
 `;
   }
   return `${JSON.stringify(config, null, 2)}
 `;
 }
+function getConfigObjectFormatName(format = "json") {
+  if (format === "yaml")
+    return "YAML";
+  if (format === "toml")
+    return "TOML";
+  return "JSON";
+}
 function isPlainObject(value) {
   return typeof value === "object" && value !== null && !Array.isArray(value);
 }
@@ -9520,7 +9561,7 @@ function mergeServerConfig(existingContent, serversKey, serverName, serverConfig
   if (typeof servers !== "object" || servers === null || Array.isArray(servers)) {
     return {
       status: "parse_error",
-      error: `"${serversKey}" is not a JSON object`
+      error: `"${serversKey}" is not a ${getConfigObjectFormatName(format)} object`
     };
   }
   const serversObj = servers;
@@ -9557,7 +9598,7 @@ function removeServerConfig(existingContent, serversKey, serverName, format = "j
   if (typeof servers !== "object" || servers === null || Array.isArray(servers)) {
     return {
       status: "parse_error",
-      error: `"${serversKey}" is not a JSON object`
+      error: `"${serversKey}" is not a ${getConfigObjectFormatName(format)} object`
     };
   }
   const serversObj = servers;
@@ -9623,7 +9664,7 @@ async function getConfigUninstallCheckStatus(config, fs) {
     if (typeof servers !== "object" || servers === null || Array.isArray(servers)) {
       return {
         status: "failed",
-        message: `Cannot parse ${config.configPath}: "${config.serversKey}" is not a ${config.format === "yaml" ? "YAML" : "JSON"} object. File left unchanged.`
+        message: `Cannot parse ${config.configPath}: "${config.serversKey}" is not a ${getConfigObjectFormatName(config.format)} object. File left unchanged.`
       };
     }
     const hasEntry = getMatchingServerKeys(servers, config.serverName).length > 0;
@@ -9688,7 +9729,7 @@ var ALREADY_EXISTS_PATTERNS = [
 var ALREADY_ABSENT_PATTERNS = [
   /(?:plugin|extension|server|mcp server)\s+["']?githits["']?\s+(?:was\s+)?not\s+found/i,
   /["']?githits["']?\s+(?:plugin|extension|server)?\s*(?:does\s+not\s+exist|is\s+not\s+installed|not\s+installed)/i,
-  /(?:package\s+)?["']?pi-mcp-adapter["']?\s+(?:is\s+)?not\s+installed/i,
+  /(?:package\s+)?["']?pi-mcp-adapter["']?\s+(?:(?:is\s+)?not\s+installed|not\s+found)/i,
   /unknown\s+(?:plugin|extension|server)\s+["']?githits["']?/i,
   /marketplace\s+["']?githits-plugins["']?\s+(?:was\s+)?not\s+found/i
 ];
@@ -9733,15 +9774,15 @@ async function executeCliUninstallCommand(cmd, execService) {
   try {
     const result = await execService.exec(cmd.command, cmd.args);
     const combined = `${result.stdout} ${result.stderr}`;
-    if (result.exitCode === 0) {
-      return { status: "removed", message: "Removed successfully" };
-    }
     if (isAlreadyAbsentOutput(combined)) {
       return {
         status: "not_configured",
         message: `GitHits not configured via ${cmd.command}`
       };
     }
+    if (result.exitCode === 0) {
+      return { status: "removed", message: "Removed successfully" };
+    }
     const detail = result.stderr.trim() || result.stdout.trim();
     return {
       status: "failed",
@@ -10045,6 +10086,48 @@ function getHermesHomeDir(fs) {
 function getHermesConfigPath(fs) {
   return fs.joinPath(getHermesHomeDir(fs), "config.yaml");
 }
+function getStandardMcpServerConfig() {
+  return {
+    command: GITHITS_MCP_COMMAND,
+    args: [...GITHITS_MCP_ARGS]
+  };
+}
+function getVsCodeMcpServerConfig() {
+  return {
+    type: "stdio",
+    ...getStandardMcpServerConfig()
+  };
+}
+function getProjectPath(fs) {
+  return fs.getCwd();
+}
+function getProjectJsonConfig(fs, relativePath, serversKey, serverConfig = getStandardMcpServerConfig()) {
+  return {
+    method: "config-file",
+    configPath: fs.joinPath(getProjectPath(fs), ...relativePath),
+    serversKey,
+    serverName: GITHITS_SERVER_NAME,
+    serverConfig
+  };
+}
+function getUnsupportedProjectSetup(reason) {
+  return { supported: false, reason };
+}
+function getAgentSetupConfig(agent, fs, scope = "user", context) {
+  if (scope === "project") {
+    if (agent.projectSetup?.supported) {
+      return agent.projectSetup.getSetupConfig(fs, context);
+    }
+    return null;
+  }
+  return agent.getSetupConfig(fs, context);
+}
+function getProjectSetupUnsupportedReason(agent) {
+  if (agent.projectSetup?.supported) {
+    return null;
+  }
+  return agent.projectSetup?.reason ?? "project-level MCP config not verified";
+}
 function getOpenCodeDesktopDetectPaths(fs) {
   const userDataRoot = getUserDataRoot(fs);
   return [
@@ -10155,7 +10238,11 @@ var claudeCode = {
         args: ["plugin", "marketplace", "remove", CLAUDE_GITHITS_MARKETPLACE]
       }
     ]
-  })
+  }),
+  projectSetup: {
+    supported: true,
+    getSetupConfig: (fs) => getProjectJsonConfig(fs, [".mcp.json"], "mcpServers")
+  }
 };
 var cursor = {
   name: "Cursor",
@@ -10168,11 +10255,12 @@ var cursor = {
     configPath: fs.joinPath(fs.getHomeDir(), ".cursor", "mcp.json"),
     serversKey: "mcpServers",
     serverName: GITHITS_SERVER_NAME,
-    serverConfig: {
-      command: GITHITS_MCP_COMMAND,
-      args: [...GITHITS_MCP_ARGS]
-    }
-  })
+    serverConfig: getStandardMcpServerConfig()
+  }),
+  projectSetup: {
+    supported: true,
+    getSetupConfig: (fs) => getProjectJsonConfig(fs, [".cursor", "mcp.json"], "mcpServers")
+  }
 };
 var windsurf = {
   name: "Windsurf",
@@ -10185,11 +10273,9 @@ var windsurf = {
     configPath: fs.joinPath(fs.getHomeDir(), ".codeium", "windsurf", "mcp_config.json"),
     serversKey: "mcpServers",
     serverName: GITHITS_SERVER_NAME,
-    serverConfig: {
-      command: GITHITS_MCP_COMMAND,
-      args: [...GITHITS_MCP_ARGS]
-    }
-  })
+    serverConfig: getStandardMcpServerConfig()
+  }),
+  projectSetup: getUnsupportedProjectSetup("project-level MCP config not verified for Windsurf")
 };
 var claudeDesktop = {
   name: "Claude Desktop",
@@ -10216,12 +10302,10 @@ var claudeDesktop = {
       configPath: fs.joinPath(appData, "claude_desktop_config.json"),
       serversKey: "mcpServers",
       serverName: GITHITS_SERVER_NAME,
-      serverConfig: {
-        command: GITHITS_MCP_COMMAND,
-        args: [...GITHITS_MCP_ARGS]
-      }
+      serverConfig: getStandardMcpServerConfig()
     };
-  }
+  },
+  projectSetup: getUnsupportedProjectSetup("Claude Desktop uses user-level desktop config")
 };
 var codexCli = {
   name: "Codex CLI",
@@ -10251,7 +10335,18 @@ var codexCli = {
         args: ["mcp", "remove", "githits"]
       }
     ]
-  })
+  }),
+  projectSetup: {
+    supported: true,
+    getSetupConfig: (fs) => ({
+      method: "config-file",
+      format: "toml",
+      configPath: fs.joinPath(getProjectPath(fs), ".codex", "config.toml"),
+      serversKey: "mcp_servers",
+      serverName: "githits",
+      serverConfig: getStandardMcpServerConfig()
+    })
+  }
 };
 var pi = {
   name: "Pi",
@@ -10284,8 +10379,7 @@ var pi = {
           serversKey: "mcpServers",
           serverName: GITHITS_SERVER_NAME,
           serverConfig: {
-            command: GITHITS_MCP_COMMAND,
-            args: [...GITHITS_MCP_ARGS],
+            ...getStandardMcpServerConfig(),
             lifecycle: "eager"
           }
         }
@@ -10321,6 +10415,32 @@ var pi = {
         }
       ]
     };
+  },
+  projectSetup: {
+    supported: true,
+    getSetupConfig: (fs, context) => {
+      const piCommand = context?.command ?? "pi";
+      return {
+        method: "composite",
+        steps: [
+          {
+            method: "cli",
+            commands: [
+              {
+                command: piCommand,
+                args: ["install", "npm:pi-mcp-adapter"]
+              }
+            ],
+            checkCommand: {
+              command: piCommand,
+              args: ["list"],
+              configuredPattern: PI_ADAPTER_CONFIGURED_PATTERN
+            }
+          },
+          getProjectJsonConfig(fs, [".mcp.json"], "mcpServers")
+        ]
+      };
+    }
   }
 };
 var vscode = {
@@ -10339,11 +10459,12 @@ var vscode = {
       configPath: fs.joinPath(appData, "User", "mcp.json"),
       serversKey: "servers",
       serverName: GITHITS_SERVER_NAME,
-      serverConfig: {
-        command: GITHITS_MCP_COMMAND,
-        args: [...GITHITS_MCP_ARGS]
-      }
+      serverConfig: getVsCodeMcpServerConfig()
     };
+  },
+  projectSetup: {
+    supported: true,
+    getSetupConfig: (fs) => getProjectJsonConfig(fs, [".vscode", "mcp.json"], "servers", getVsCodeMcpServerConfig())
   }
 };
 var cline = {
@@ -10357,11 +10478,9 @@ var cline = {
     configPath: fs.joinPath(fs.getHomeDir(), ".cline", "data", "settings", "cline_mcp_settings.json"),
     serversKey: "mcpServers",
     serverName: GITHITS_SERVER_NAME,
-    serverConfig: {
-      command: GITHITS_MCP_COMMAND,
-      args: [...GITHITS_MCP_ARGS]
-    }
-  })
+    serverConfig: getStandardMcpServerConfig()
+  }),
+  projectSetup: getUnsupportedProjectSetup("Cline MCP settings are documented as user-level config; project MCP auto-load not verified")
 };
 var geminiCli = {
   name: "Gemini CLI",
@@ -10397,7 +10516,11 @@ var geminiCli = {
         args: ["extensions", "uninstall", "githits"]
       }
     ]
-  })
+  }),
+  projectSetup: {
+    supported: true,
+    getSetupConfig: (fs) => getProjectJsonConfig(fs, [".gemini", "settings.json"], "mcpServers")
+  }
 };
 async function isGeminiExtensionInstalledFromFilesystem(fs) {
   const extensionManifestPath = fs.joinPath(fs.getHomeDir(), ".gemini", "extensions", "githits", "gemini-extension.json");
@@ -10414,11 +10537,9 @@ var googleAntigravity = {
     configPath: fs.joinPath(fs.getHomeDir(), ".gemini", "antigravity", "mcp_config.json"),
     serversKey: "mcpServers",
     serverName: GITHITS_SERVER_NAME,
-    serverConfig: {
-      command: GITHITS_MCP_COMMAND,
-      args: [...GITHITS_MCP_ARGS]
-    }
-  })
+    serverConfig: getStandardMcpServerConfig()
+  }),
+  projectSetup: getUnsupportedProjectSetup("Google Antigravity project-level MCP config not verified")
 };
 var openCode = {
   name: "OpenCode",
@@ -10437,7 +10558,15 @@ var openCode = {
       command: [...GITHITS_MCP_INVOCATION],
       enabled: true
     }
-  })
+  }),
+  projectSetup: {
+    supported: true,
+    getSetupConfig: (fs) => getProjectJsonConfig(fs, ["opencode.json"], "mcp", {
+      type: "local",
+      command: [...GITHITS_MCP_INVOCATION],
+      enabled: true
+    })
+  }
 };
 var hermesAgent = {
   name: "Hermes Agent",
@@ -10452,11 +10581,9 @@ var hermesAgent = {
     configPath: getHermesConfigPath(fs),
     serversKey: "mcp_servers",
     serverName: GITHITS_SERVER_NAME,
-    serverConfig: {
-      command: GITHITS_MCP_COMMAND,
-      args: [...GITHITS_MCP_ARGS]
-    }
-  })
+    serverConfig: getStandardMcpServerConfig()
+  }),
+  projectSetup: getUnsupportedProjectSetup("Hermes Agent project-level MCP config not verified")
 };
 var agentDefinitions = [
   claudeCode,
@@ -10472,7 +10599,7 @@ var agentDefinitions = [
   openCode,
   hermesAgent
 ];
-async function scanSingleAgent(agent, fs, execService) {
+async function scanSingleAgent(agent, fs, execService, scope) {
   let detected = false;
   let setupContext;
   if (agent.detectCommand) {
@@ -10523,7 +10650,14 @@ async function scanSingleAgent(agent, fs, execService) {
   if (!detected) {
     return { status: "not_detected", agent };
   }
-  const config = agent.getSetupConfig(fs, setupContext);
+  const config = getAgentSetupConfig(agent, fs, scope, setupContext);
+  if (!config) {
+    return {
+      status: "unsupported",
+      agent,
+      reason: getProjectSetupUnsupportedReason(agent) ?? "project-level MCP config not verified"
+    };
+  }
   const scannedAgent = {
     ...agent,
     resolvedSetupConfig: config,
@@ -10552,10 +10686,11 @@ async function scanAgents(definitions, fs, execService, options = {}) {
   const result = {
     needsSetup: [],
     alreadyConfigured: [],
-    notDetected: []
+    notDetected: [],
+    unsupported: []
   };
   let completed = 0;
-  const outcomes = await Promise.all(definitions.map((agent) => scanSingleAgent(agent, fs, execService).then((outcome) => {
+  const outcomes = await Promise.all(definitions.map((agent) => scanSingleAgent(agent, fs, execService, options.scope ?? "user").then((outcome) => {
     completed += 1;
     options.onProgress?.({
       completed,
@@ -10569,6 +10704,11 @@ async function scanAgents(definitions, fs, execService, options = {}) {
       result.alreadyConfigured.push(outcome.agent);
     } else if (outcome.status === "needs_setup") {
       result.needsSetup.push(outcome.agent);
+    } else if (outcome.status === "unsupported") {
+      result.unsupported.push({
+        agent: outcome.agent,
+        reason: outcome.reason
+      });
     } else {
       result.notDetected.push(outcome.agent);
     }
@@ -10594,6 +10734,9 @@ function createInitLoginOutput() {
 function getResolvedSetupConfig(agent, fileSystemService) {
   return agent.resolvedSetupConfig ?? agent.getSetupConfig(fileSystemService, agent.resolvedSetupContext);
 }
+function getLegacyProjectSetupStatePath(fileSystemService) {
+  return fileSystemService.joinPath(fileSystemService.getCwd(), ".githits", "init", "project-setup.json");
+}
 function getPiConfigFileUninstall(agent, fileSystemService) {
   if (agent.id !== "pi") {
     return null;
@@ -10609,13 +10752,27 @@ function formatCommand(command, useColors) {
   return colorizeBrand(command, "secondary", useColors, { bold: true });
 }
 var AGENT_SAFE_CLI = "npx -y githits@latest";
-var AGENT_DETECT_COMMAND = `${AGENT_SAFE_CLI} init --detect-agents`;
-var AGENT_INSTALL_COMMAND = `${AGENT_SAFE_CLI} init --install-agents`;
 var AGENT_LOGIN_COMMAND = `${AGENT_SAFE_CLI} login`;
 var AGENT_LOGIN_NO_BROWSER_COMMAND = `${AGENT_SAFE_CLI} login --no-browser`;
 var AGENTIC_INIT_YES_WARNING = "Do not run `githits init -y` or `githits init --yes` unless the user explicitly asks to configure every detected tool.";
-var AGENTIC_INIT_VERIFY_INSTRUCTION = "After a successful --install-agents run, verify with --detect-agents --json instead of running init again.";
-var AGENTIC_INIT_JSON_VERIFY_INSTRUCTION = "Do not run init again after a successful --install-agents run; verify with --detect-agents --json instead.";
+function getAgentDetectCommand(scope) {
+  return `${AGENT_SAFE_CLI} init ${scope === "project" ? "--project " : ""}--detect-agents`;
+}
+function getAgentInstallCommand(scope) {
+  return `${AGENT_SAFE_CLI} init ${scope === "project" ? "--project " : ""}--install-agents`;
+}
+function getAgenticVerifyCommand(scope) {
+  return `${getAgentDetectCommand(scope)} --json`;
+}
+function getAgenticVerifyInstruction(scope) {
+  return `After a successful --install-agents run, verify with ${getAgenticVerifyCommand(scope)} instead of running init again.`;
+}
+function getAgenticJsonVerifyInstruction(scope) {
+  return `Do not run init again after a successful --install-agents run; verify with ${getAgenticVerifyCommand(scope)} instead.`;
+}
+function formatInstallCommand(ids, scope) {
+  return `${getAgentInstallCommand(scope)} ${ids.join(",")}`;
+}
 function printReadyNextSteps() {
   console.log("  GitHits is now connected to your coding agents.");
   console.log();
@@ -10648,6 +10805,22 @@ function printAuthNotCheckedNextSteps(useColors) {
   console.log("  If your agent asks you to sign in, run:");
   console.log(`    ${formatCommand("npx githits@latest login", useColors)}`);
 }
+function printProjectAuthRequiredNextSteps(useColors) {
+  console.log("  GitHits MCP is configured for this project, but sign-in is still needed.");
+  console.log();
+  console.log("  Open an MCP-compatible coding agent in this project so it loads the project config.");
+  console.log();
+  console.log("  Sign in when you're ready:");
+  console.log(`    ${formatCommand("npx githits@latest login", useColors)}`);
+}
+function printProjectAuthNotCheckedNextSteps(useColors) {
+  console.log("  GitHits MCP is configured for this project. Sign-in was not checked.");
+  console.log();
+  console.log("  Open an MCP-compatible coding agent in this project so it loads the project config.");
+  console.log();
+  console.log("  If your agent asks you to sign in, run:");
+  console.log(`    ${formatCommand("npx githits@latest login", useColors)}`);
+}
 function printAgenticLoginInstructions(useColors) {
   console.log("  Authentication is still required before agents can use GitHits.");
   console.log();
@@ -10678,25 +10851,38 @@ function printNonInteractiveInitGuidance(useColors) {
   console.log();
   console.log("  If you are an AI coding agent helping a user install GitHits:");
   console.log();
-  console.log("  1. Run:");
-  console.log(`     ${formatCommand(AGENT_DETECT_COMMAND, useColors)}`);
+  console.log("  1. Ask the user whether GitHits should be installed for:");
+  console.log("     - this user account on this machine, or");
+  console.log("     - only this project/repo via project-local MCP files.");
+  console.log();
+  console.log("  2. For user-level install, run:");
+  console.log(`     ${formatCommand(getAgentDetectCommand("user"), useColors)}`);
   console.log();
-  console.log("  2. Show the detected tools to the user.");
+  console.log("     For project-level install, run:");
+  console.log(`     ${formatCommand(getAgentDetectCommand("project"), useColors)}`);
   console.log();
-  console.log("  3. Ask which tools should receive the GitHits MCP server.");
+  console.log("  3. Show the detected tools to the user.");
   console.log();
-  console.log("  4. Only after approval, run:");
-  console.log(`     ${formatCommand(`${AGENT_INSTALL_COMMAND} <ids>`, useColors)}`);
+  console.log("  4. Ask which tools should receive the GitHits MCP server.");
+  console.log();
+  console.log("     For project-level install, explain that config files are written into this repo and may be committed.");
+  console.log();
+  console.log("  5. Only after approval, run the matching install command:");
+  console.log(`     ${formatCommand(`${getAgentInstallCommand("user")} <ids>`, useColors)}`);
+  console.log(`     ${formatCommand(`${getAgentInstallCommand("project")} <ids>`, useColors)}`);
   console.log();
   console.log(`  ${AGENTIC_INIT_YES_WARNING}`);
-  console.log(`  ${AGENTIC_INIT_VERIFY_INSTRUCTION}`);
+  console.log(`  ${getAgenticVerifyInstruction("user")}`);
+  console.log(`  ${getAgenticVerifyInstruction("project")}`);
 }
 function printNonInteractiveYesRejected(useColors) {
   console.error("Non-interactive `githits init --yes` is not supported because it can configure tools without explicit per-tool approval.");
   console.error();
   console.error("Use the agent-safe staged flow instead:");
-  console.error(`  ${formatCommand(AGENT_DETECT_COMMAND, useColors)}`);
-  console.error(`  ${formatCommand(`${AGENT_INSTALL_COMMAND} <ids>`, useColors)}`);
+  console.error(`  ${formatCommand(getAgentDetectCommand("user"), useColors)}`);
+  console.error(`  ${formatCommand(`${getAgentInstallCommand("user")} <ids>`, useColors)}`);
+  console.error(`  ${formatCommand(getAgentDetectCommand("project"), useColors)}`);
+  console.error(`  ${formatCommand(`${getAgentInstallCommand("project")} <ids>`, useColors)}`);
   process.exitCode = 1;
 }
 var GITHITS_ASCII_LOGO = String.raw`
@@ -10787,6 +10973,30 @@ var INIT_INTENT_CHOICES = [
     description: "Leave setup without making changes."
   }
 ];
+var INIT_SCOPE_CHOICES = [
+  {
+    name: "User-level config",
+    value: "user",
+    description: "Configure GitHits for your detected tools on this machine."
+  },
+  {
+    name: "Project-level config",
+    value: "project",
+    description: "Configure project-local MCP files for tools that support workspace config."
+  }
+];
+var INIT_UNINSTALL_SCOPE_CHOICES = [
+  {
+    name: "User-level config",
+    value: "user",
+    description: "Remove GitHits from detected tools on this machine."
+  },
+  {
+    name: "Project-level config",
+    value: "project",
+    description: "Remove GitHits from supported project-local MCP files."
+  }
+];
 var AUTH_RECOVERY_CHOICES = [
   { name: "Retry sign in", value: "retry" },
   {
@@ -10861,8 +11071,9 @@ function printSkillsInstructions(useColors) {
   console.log(`    ${formatCommand("npx githits@latest login", useColors)}`);
   console.log();
 }
-function startSafeInitScan(fileSystemService, execService, onProgress) {
+function startSafeInitScan(fileSystemService, execService, scope = "user", onProgress) {
   return scanAgents(agentDefinitions, fileSystemService, execService, {
+    scope,
     onProgress
   }).then((scan) => ({ ok: true, scan })).catch((error2) => ({
     ok: false,
@@ -10949,50 +11160,85 @@ function buildInitAgentChoices(scan) {
     }))
   ];
 }
-function printScanSummary(scan, useColors) {
-  const detected = scan.needsSetup.length + scan.alreadyConfigured.length;
+function printScanSummary(scan, useColors, scope = "user") {
+  const detected = scan.needsSetup.length + scan.alreadyConfigured.length + scan.unsupported.length;
+  const projectSupported = scan.needsSetup.length + scan.alreadyConfigured.length;
   for (const agent of scan.alreadyConfigured) {
     printTask("success", agent.name, "already configured", useColors);
   }
   for (const agent of scan.needsSetup) {
     printTask("warning", agent.name, "needs setup", useColors);
   }
+  for (const { agent, reason } of scan.unsupported) {
+    printTask("skipped", agent.name, scope === "project" ? "no project-level config" : reason, useColors);
+  }
   if (scan.notDetected.length > 0) {
     printTask("skipped", `${scan.notDetected.length} supported tool${scan.notDetected.length !== 1 ? "s" : ""} not found`, formatAgentNames(scan.notDetected), useColors);
   }
   if (detected > 0) {
     console.log();
-    console.log(`    Found ${detected} supported tool${detected !== 1 ? "s" : ""}.`);
+    if (scope === "project") {
+      console.log(`    Found ${detected} tool${detected !== 1 ? "s" : ""}. ${projectSupported} support${projectSupported === 1 ? "s" : ""} project-level config.`);
+    } else {
+      console.log(`    Found ${detected} supported tool${detected !== 1 ? "s" : ""}.`);
+    }
   }
 }
+function printProjectScopeExplanation(useColors) {
+  console.log();
+  console.log(`  ${warning("Project-level config is available for some tools.", useColors)}`);
+  console.log("  Tools without project-level config are shown below but won't be selected.");
+}
 function buildStagedAgentEntries(scan) {
   const statuses = new Map;
-  for (const agent of scan.needsSetup)
-    statuses.set(agent.id, "needs_setup");
+  for (const agent of scan.needsSetup) {
+    statuses.set(agent.id, { status: "needs_setup" });
+  }
   for (const agent of scan.alreadyConfigured) {
-    statuses.set(agent.id, "already_configured");
-  }
-  for (const agent of scan.notDetected)
-    statuses.set(agent.id, "not_detected");
-  return agentDefinitions.map((agent) => ({
-    id: agent.id,
-    name: agent.name,
-    status: statuses.get(agent.id) ?? "not_detected"
-  }));
+    statuses.set(agent.id, { status: "already_configured" });
+  }
+  for (const agent of scan.notDetected) {
+    statuses.set(agent.id, { status: "not_detected" });
+  }
+  for (const { agent, reason } of scan.unsupported) {
+    statuses.set(agent.id, {
+      status: "unsupported_project_config",
+      reason
+    });
+  }
+  return agentDefinitions.map((agent) => {
+    const entry = statuses.get(agent.id);
+    return {
+      id: agent.id,
+      name: agent.name,
+      status: entry?.status ?? "not_detected",
+      ...entry?.reason ? { reason: entry.reason } : {}
+    };
+  });
 }
-function printAgenticDetectSummary(scan, useColors) {
+function printAgenticDetectSummary(scan, useColors, scope) {
   const entries = buildStagedAgentEntries(scan);
   const detected = entries.filter((entry) => entry.status !== "not_detected");
   const installable = entries.filter((entry) => entry.status === "needs_setup");
+  const unsupported = entries.filter((entry) => entry.status === "unsupported_project_config");
+  const configured = entries.filter((entry) => entry.status === "already_configured");
   const notDetected = entries.filter((entry) => entry.status === "not_detected");
-  console.log("Detected supported tools:");
+  console.log(`Detected tools (${scope === "project" ? "project-level" : "user-level"} install):`);
   console.log();
+  if (scope === "project") {
+    console.log("  Project-level install writes MCP config files into this repo. These files may be committed.");
+    console.log("  Tools without verified project config are shown as unsupported and cannot be installed with --project.");
+    console.log();
+  }
   if (detected.length === 0) {
     console.log("  None detected.");
   } else {
     console.log("  ID                 Tool                  Status");
     for (const entry of detected) {
-      console.log(`  ${entry.id.padEnd(18)} ${entry.name.padEnd(21)} ${entry.status.replace("_", " ")}`);
+      console.log(`  ${entry.id.padEnd(18)} ${entry.name.padEnd(21)} ${entry.status.replaceAll("_", " ")}`);
+      if (entry.status === "unsupported_project_config" && entry.reason) {
+        console.log(`  ${"".padEnd(18)} ${"".padEnd(21)} ${entry.reason}`);
+      }
     }
   }
   console.log();
@@ -11007,12 +11253,25 @@ function printAgenticDetectSummary(scan, useColors) {
     return;
   }
   if (installable.length === 0) {
+    if (scope === "project" && unsupported.length > 0) {
+      console.log("No detected tools can be installed with project-level config.");
+      console.log();
+      console.log("Next step for agents:");
+      if (configured.length > 0) {
+        console.log("  Tell the user GitHits is already configured for the detected project-configurable tools.");
+      }
+      console.log("  Tell the user the other detected tools do not have verified project-level MCP support.");
+      console.log(`  Offer user-level install with ${getAgentDetectCommand("user")} if they want GitHits for those tools.`);
+      console.log(`  ${AGENTIC_INIT_YES_WARNING}`);
+      console.log(`  Do not run init again as a verification step; use ${getAgenticVerifyCommand(scope)} if verification is needed.`);
+      return;
+    }
     console.log("No detected tools need setup.");
     console.log();
     console.log("Next step for agents:");
     console.log("  Tell the user that GitHits is already configured for detected tools.");
     console.log(`  ${AGENTIC_INIT_YES_WARNING}`);
-    console.log("  Do not run init again as a verification step.");
+    console.log(`  Do not run init again as a verification step; use ${getAgenticVerifyCommand(scope)} if verification is needed.`);
     return;
   }
   const installableIds = installable.map((entry) => entry.id);
@@ -11022,27 +11281,86 @@ function printAgenticDetectSummary(scan, useColors) {
   console.log(`    "GitHits can be installed for ${installable.map((entry) => entry.name).join(", ")}. Which should I configure?"`);
   console.log();
   console.log("  If the user approves all detected tools needing setup, run:");
-  console.log(`    ${formatCommand(`${AGENT_INSTALL_COMMAND} ${installableIds.join(",")}`, useColors)}`);
+  console.log(`    ${formatCommand(formatInstallCommand(installableIds, scope), useColors)}`);
+  if (scope === "project") {
+    console.log();
+    console.log("  Before running it, tell the user this writes project-local MCP files into the current repo and only configures tools with verified project support.");
+  }
   console.log();
   console.log(`  ${AGENTIC_INIT_YES_WARNING}`);
-  console.log(`  ${AGENTIC_INIT_VERIFY_INSTRUCTION}`);
+  console.log(`  ${getAgenticVerifyInstruction(scope)}`);
 }
-function printAgenticDetectJson(scan) {
+function printAgenticDetectJson(scan, scope) {
   const entries = buildStagedAgentEntries(scan);
   const installableIds = entries.filter((entry) => entry.status === "needs_setup").map((entry) => entry.id);
+  const detected = entries.filter((entry) => entry.status !== "not_detected");
+  const configured = entries.filter((entry) => entry.status === "already_configured");
+  const unsupported = entries.filter((entry) => entry.status === "unsupported_project_config");
+  const instructions = buildAgenticDetectJsonInstructions({
+    scope,
+    detectedCount: detected.length,
+    installableCount: installableIds.length,
+    configuredCount: configured.length,
+    unsupportedCount: unsupported.length
+  });
   console.log(JSON.stringify({
     mode: "detect-agents",
+    scope,
     agents: entries,
     installableIds,
-    suggestedCommand: installableIds.length > 0 ? `${AGENT_INSTALL_COMMAND} ${installableIds.join(",")}` : null,
-    instructions: [
+    suggestedCommand: installableIds.length > 0 ? formatInstallCommand(installableIds, scope) : null,
+    instructions
+  }, null, 2));
+}
+function buildAgenticDetectJsonInstructions(input) {
+  const {
+    scope,
+    detectedCount,
+    installableCount,
+    configuredCount,
+    unsupportedCount
+  } = input;
+  if (detectedCount === 0) {
+    return [
+      "No supported AI coding tools were detected.",
+      "Tell the user to install a supported coding tool, then run detection again."
+    ];
+  }
+  if (installableCount === 0) {
+    if (scope === "project" && unsupportedCount > 0) {
+      return [
+        "Show detected tools to the user.",
+        ...configuredCount > 0 ? [
+          "Explain that GitHits is already configured for detected project-configurable tools."
+        ] : [
+          "Explain that no detected tools have verified project-level MCP support."
+        ],
+        "Explain that tools with unsupported_project_config status cannot be installed with --project.",
+        "Do not ask the user to choose project install IDs.",
+        `Offer user-level detection with ${getAgentDetectCommand("user")} if they want GitHits for unsupported project tools.`,
+        AGENTIC_INIT_YES_WARNING,
+        getAgenticJsonVerifyInstruction(scope)
+      ];
+    }
+    return [
       "Show detected tools to the user.",
-      "Ask which tools should receive the GitHits MCP server.",
-      "Only run --install-agents with user-approved IDs.",
+      "Tell the user that GitHits is already configured for detected tools.",
+      "Do not ask the user to choose install IDs.",
       AGENTIC_INIT_YES_WARNING,
-      AGENTIC_INIT_JSON_VERIFY_INSTRUCTION
-    ]
-  }, null, 2));
+      getAgenticJsonVerifyInstruction(scope)
+    ];
+  }
+  return [
+    "Show detected tools to the user.",
+    ...scope === "project" ? [
+      "Explain that project-level install writes MCP config files into the current repo and those files may be committed.",
+      "Do not offer agent IDs with unsupported_project_config status for project install."
+    ] : [],
+    "Ask which tools should receive the GitHits MCP server.",
+    "Only run --install-agents with user-approved IDs.",
+    AGENTIC_INIT_YES_WARNING,
+    getAgenticJsonVerifyInstruction(scope)
+  ];
 }
 function getStagedModeCount(options) {
   return [
@@ -11086,8 +11404,10 @@ function findAgentsByIds(scan, ids) {
 }
 function validateInstallAgentIds(scan, ids) {
   const supportedIds = new Set(agentDefinitions.map((agent) => agent.id));
-  const detectedIds = [...scan.needsSetup, ...scan.alreadyConfigured].map((agent) => agent.id);
+  const installableAgents = [...scan.needsSetup, ...scan.alreadyConfigured];
+  const detectedIds = installableAgents.map((agent) => agent.id);
   const detectedIdSet = new Set(detectedIds);
+  const unsupported = new Map(scan.unsupported.map(({ agent, reason }) => [agent.id, reason]));
   if (ids.length === 0) {
     return {
       ok: false,
@@ -11103,6 +11423,15 @@ function validateInstallAgentIds(scan, ids) {
       detectedIds
     };
   }
+  const unsupportedIds = ids.filter((id) => unsupported.has(id));
+  if (unsupportedIds.length > 0) {
+    const details = unsupportedIds.map((id) => `${id}: ${unsupported.get(id)}`).join("; ");
+    return {
+      ok: false,
+      message: `Agent ID${unsupportedIds.length !== 1 ? "s" : ""} cannot use project-level install: ${details}.`,
+      detectedIds
+    };
+  }
   const undetected = ids.filter((id) => !detectedIdSet.has(id));
   if (undetected.length > 0) {
     return {
@@ -11125,6 +11454,17 @@ function printInstallValidationFailure(failure, json) {
   }
   process.exitCode = 1;
 }
+function failUnknownInitAction(action) {
+  failInitArgument(`Unknown init action: ${action}. Use "githits init uninstall" to remove GitHits MCP config.`, false);
+}
+async function resolveProjectSetupScope(options, fileSystemService) {
+  const projectPath = fileSystemService.getCwd();
+  if (!await fileSystemService.isDirectory(projectPath)) {
+    failInitArgument(`Current directory does not exist or is not a directory: ${projectPath}`, options.json);
+    return null;
+  }
+  return { projectPath };
+}
 function hasUsableInstallOutcome(outcomes) {
   return outcomes.some((outcome) => outcome.status === "success" || outcome.status === "already_configured");
 }
@@ -11162,46 +11502,54 @@ function buildAgenticInstallAuthPayload(authStatus) {
     noBrowserCommand: AGENT_LOGIN_NO_BROWSER_COMMAND
   };
 }
-function buildAgenticInstallInstructions(authStatus) {
+function buildAgenticInstallInstructions(authStatus, scope) {
   if (authStatus === "authenticated") {
-    return ["Open a new coding agent session so it reloads MCP config."];
+    return [
+      scope === "project" ? "Open a new coding agent session in this project so it reloads project MCP config." : "Open a new coding agent session so it reloads MCP config.",
+      getAgenticJsonVerifyInstruction(scope)
+    ];
   }
   if (authStatus === "required") {
     return [
       `Ask the user before running ${AGENT_LOGIN_COMMAND}.`,
       "Browser sign-in happens outside chat and terminal input.",
-      "Do not ask the user to paste passwords, tokens, cookies, or OAuth codes into chat."
+      "Do not ask the user to paste passwords, tokens, cookies, or OAuth codes into chat.",
+      getAgenticJsonVerifyInstruction(scope)
     ];
   }
   return [
     "Sign-in status was not checked.",
-    `If the user is not already signed in, ask before running ${AGENT_LOGIN_COMMAND}.`
+    `If the user is not already signed in, ask before running ${AGENT_LOGIN_COMMAND}.`,
+    getAgenticJsonVerifyInstruction(scope)
   ];
 }
-function printAgenticInstallJson(outcomes, authStatus) {
+function printAgenticInstallJson(outcomes, authStatus, scope) {
   const canAuthenticate = hasUsableInstallOutcome(outcomes);
   console.log(JSON.stringify({
     mode: "install-agents",
+    scope,
     outcomes,
     auth: canAuthenticate ? buildAgenticInstallAuthPayload(authStatus) : {
       required: false,
       status: "not_applicable",
       reason: "Fix installation errors before starting sign-in."
     },
-    instructions: canAuthenticate ? buildAgenticInstallInstructions(authStatus) : ["Fix installation errors before asking the user to sign in."]
+    instructions: canAuthenticate ? buildAgenticInstallInstructions(authStatus, scope) : ["Fix installation errors before asking the user to sign in."]
   }, null, 2));
 }
 async function runDetectAgentsMode(options, fileSystemService, execService, useColors) {
-  const scan = await scanAgents(agentDefinitions, fileSystemService, execService);
+  const scope = options.project ? "project" : "user";
+  const scan = await scanAgents(agentDefinitions, fileSystemService, execService, { scope });
   if (options.json) {
-    printAgenticDetectJson(scan);
+    printAgenticDetectJson(scan, scope);
     return;
   }
-  printAgenticDetectSummary(scan, useColors);
+  printAgenticDetectSummary(scan, useColors, scope);
 }
 async function runInstallAgentsMode(options, fileSystemService, execService, createLoginDeps, useColors) {
+  const scope = options.project ? "project" : "user";
   const requestedIds = parseAgentIdList(options.installAgents);
-  const scan = await scanAgents(agentDefinitions, fileSystemService, execService);
+  const scan = await scanAgents(agentDefinitions, fileSystemService, execService, { scope });
   const validation = validateInstallAgentIds(scan, requestedIds);
   if (!validation.ok) {
     printInstallValidationFailure(validation, options.json);
@@ -11212,7 +11560,7 @@ async function runInstallAgentsMode(options, fileSystemService, execService, cre
     console.log("Installing GitHits MCP:");
     console.log();
   }
-  const outcomes = await installSelectedAgents(agents, scan, fileSystemService, execService, useColors, !options.json);
+  const outcomes = await installSelectedAgents(agents, scan, fileSystemService, execService, useColors, !options.json, scope);
   const failed = outcomes.filter((outcome) => outcome.status === "failed");
   const canAuthenticate = hasUsableInstallOutcome(outcomes);
   const authStatus = canAuthenticate ? await getStagedInstallAuthStatus(createLoginDeps) : "not_checked";
@@ -11220,7 +11568,7 @@ async function runInstallAgentsMode(options, fileSystemService, execService, cre
     process.exitCode = 1;
   }
   if (options.json) {
-    printAgenticInstallJson(outcomes, authStatus);
+    printAgenticInstallJson(outcomes, authStatus, scope);
     return;
   }
   console.log();
@@ -11235,12 +11583,19 @@ async function runInstallAgentsMode(options, fileSystemService, execService, cre
   console.log();
   if (canAuthenticate) {
     if (authStatus === "authenticated") {
-      printAgenticAlreadyAuthenticated();
+      if (scope === "project") {
+        console.log("  GitHits MCP is installed for this project and you are already signed in.");
+        console.log();
+        console.log("  Open a new coding agent session in this project so it reloads project MCP config.");
+      } else {
+        printAgenticAlreadyAuthenticated();
+      }
     } else if (authStatus === "required") {
       printAgenticLoginInstructions(useColors);
     } else {
       printAgenticAuthNotChecked(useColors);
     }
+    console.log(`  ${getAgenticVerifyInstruction(scope)}`);
   } else {
     console.log("Fix installation errors before starting sign-in.");
   }
@@ -11355,66 +11710,460 @@ function printPostSetupNextSteps(authStatus, useColors) {
     printAuthNotCheckedNextSteps(useColors);
   }
 }
-async function verifyAgentConfigured(agent, fileSystemService, execService) {
-  const postCheck = await scanAgents([agent], fileSystemService, execService);
-  if (postCheck.alreadyConfigured.some((a) => a.id === agent.id)) {
-    return { ok: true };
+function printProjectNextSteps(authStatus, useColors) {
+  printSection(5, shouldPrintReady(authStatus) ? "Ready" : "Next Steps", useColors);
+  if (shouldPrintReady(authStatus)) {
+    printReadyNextSteps();
+  } else if (authStatus === "failed_continue") {
+    printProjectAuthRequiredNextSteps(useColors);
+  } else {
+    printProjectAuthNotCheckedNextSteps(useColors);
   }
-  if (postCheck.needsSetup.some((a) => a.id === agent.id)) {
-    return {
-      ok: false,
-      message: `${agent.name} verification failed: not configured after setup.`
-    };
+}
+function printScopedNextSteps(scope, authStatus, useColors) {
+  if (scope === "project") {
+    printProjectNextSteps(authStatus, useColors);
+    return;
   }
-  return {
-    ok: false,
-    message: `${agent.name} verification failed: agent not detected after setup.`
-  };
+  printPostSetupNextSteps(authStatus, useColors);
 }
-async function executeAgentSetupWithVerification(agent, fileSystemService, execService) {
-  const config = getResolvedSetupConfig(agent, fileSystemService);
-  let result = config.method === "cli" ? await executeCliSetup(config, execService) : config.method === "config-file" ? await executeConfigFileSetup(config, fileSystemService) : await executeCompositeSetup(config, fileSystemService, execService);
-  if (result.status === "success" || result.status === "already_configured") {
-    const verification = await verifyAgentConfigured(agent, fileSystemService, execService);
-    if (!verification.ok) {
-      result = {
-        status: "failed",
-        message: agent.id === "gemini-cli" ? "Gemini installation did not complete. Retry, or run: gemini extensions install --consent https://github.com/githits-com/githits-cli" : verification.message ?? `${agent.name} verification failed after setup.`
-      };
-    }
+function getConfigFileSetups(setup) {
+  if (setup.method === "config-file") {
+    return [setup];
   }
-  return result;
+  if (setup.method === "composite") {
+    return setup.steps.filter((step) => step.method === "config-file");
+  }
+  return [];
 }
-async function installSelectedAgents(agents, scan, fileSystemService, execService, useColors, printResults) {
-  const alreadyConfiguredIds = new Set(scan.alreadyConfigured.map((agent) => agent.id));
-  const outcomes = [];
-  const installTasks = createInstallTaskReporter(useColors);
+function getTomlSetups(setup) {
+  return getConfigFileSetups(setup).filter((step) => step.format === "toml");
+}
+async function hasExistingConfigContent(config, fileSystemService) {
+  try {
+    return (await fileSystemService.readFile(config.configPath)).trim().length > 0;
+  } catch {
+    return false;
+  }
+}
+async function printTomlRewriteWarnings(agents, fileSystemService, useColors) {
+  const seen = new Set;
   for (const agent of agents) {
-    if (alreadyConfiguredIds.has(agent.id)) {
-      outcomes.push({
-        id: agent.id,
-        name: agent.name,
-        status: "already_configured"
-      });
-      if (printResults) {
-        printTask("warning", agent.name, "already configured", useColors);
-      }
-      continue;
-    }
-    const finishTask = printResults ? installTasks.start(agent.name) : () => {};
-    let result;
-    try {
-      result = await executeAgentSetupWithVerification(agent, fileSystemService, execService);
-    } finally {
-      finishTask();
+    const setup = getResolvedSetupConfig(agent, fileSystemService);
+    for (const config of getTomlSetups(setup)) {
+      if (seen.has(config.configPath))
+        continue;
+      if (!await hasExistingConfigContent(config, fileSystemService))
+        continue;
+      seen.add(config.configPath);
+      printTask("warning", config.configPath, "existing TOML comments/formatting will not be preserved", useColors);
     }
-    outcomes.push({
-      id: agent.id,
-      name: agent.name,
-      status: result.status,
-      message: result.status === "failed" ? result.message : undefined
-    });
-    if (!printResults) {
+  }
+}
+async function getProjectUninstallPlan(fileSystemService) {
+  const seenConfig = new Set;
+  const plan = {
+    configRemovals: []
+  };
+  for (const agent of agentDefinitions) {
+    const setup = getAgentSetupConfig(agent, fileSystemService, "project");
+    if (!setup)
+      continue;
+    for (const configSetup of getConfigFileSetups(setup)) {
+      const key = `${configSetup.configPath}\x00${configSetup.serversKey}\x00${configSetup.serverName.toLowerCase()}`;
+      if (seenConfig.has(key))
+        continue;
+      seenConfig.add(key);
+      plan.configRemovals.push(configSetup);
+    }
+  }
+  return plan;
+}
+async function cleanupLegacyProjectSetupState(fileSystemService) {
+  const statePath = getLegacyProjectSetupStatePath(fileSystemService);
+  try {
+    if (!await fileSystemService.exists(statePath)) {
+      return { removed: [], failed: [] };
+    }
+    await fileSystemService.deleteFile(statePath);
+    return { removed: [statePath], failed: [] };
+  } catch (err) {
+    return {
+      removed: [],
+      failed: [
+        {
+          path: statePath,
+          reason: `Could not remove legacy project setup marker: ${err instanceof Error ? err.message : String(err)}`
+        }
+      ]
+    };
+  }
+}
+function printProjectUninstallSummary(summary) {
+  const totalRemoved = summary.removed.length + summary.legacyRemoved.length;
+  console.log();
+  if (summary.failed.length === 0) {
+    if (summary.removed.length > 0) {
+      console.log("  Done! GitHits MCP configuration was removed from this project.");
+    } else if (summary.legacyRemoved.length > 0) {
+      console.log("  Done! Removed legacy GitHits project setup marker. No project MCP config entries were found.");
+    } else {
+      console.log("  No project GitHits MCP configuration found.");
+    }
+  } else {
+    console.log("  Project uninstall completed with errors.");
+  }
+  console.log(`  Removed ${totalRemoved} item${totalRemoved !== 1 ? "s" : ""}. Skipped ${summary.skipped.length} config path${summary.skipped.length !== 1 ? "s" : ""} without GitHits.`);
+  if (summary.failed.length > 0) {
+    console.log(`  Failed to remove ${summary.failed.length} item${summary.failed.length !== 1 ? "s" : ""}:`);
+    for (const failure of summary.failed) {
+      console.log(`    - ${failure.path}: ${failure.reason}`);
+    }
+  }
+  console.log();
+}
+async function runProjectMcpUninstall(options, deps, useColors) {
+  const { fileSystemService, promptService } = deps;
+  const isInteractive = deps.isInteractive ?? true;
+  const scope = await resolveProjectSetupScope({}, fileSystemService);
+  if (!scope)
+    return;
+  const projectPlan = await getProjectUninstallPlan(fileSystemService);
+  console.log(`
+  ${colorize("Remove GitHits from this project's MCP config.", "bold", useColors)}`);
+  console.log(`  ${colorize("Removes GitHits entries from supported project-local MCP files.", "dim", useColors)}
+`);
+  console.log(`    Project: ${scope.projectPath}`);
+  for (const setup of projectPlan.configRemovals) {
+    console.log(`    Config: ${setup.configPath}`);
+  }
+  console.log();
+  const checks = await Promise.all(projectPlan.configRemovals.map(async (setup) => ({
+    setup,
+    check: await getConfigUninstallCheckStatus(setup, fileSystemService)
+  })));
+  const configured = checks.filter((entry) => entry.check.status === "configured");
+  const failedChecks = checks.filter((entry) => entry.check.status === "failed");
+  for (const { setup, check } of failedChecks) {
+    printTask("failed", setup.configPath, check.message, useColors);
+  }
+  const skipped = checks.filter((entry) => entry.check.status === "not_configured").map((entry) => entry.setup.configPath);
+  const legacyStatePath = getLegacyProjectSetupStatePath(fileSystemService);
+  const legacyProbeFailures = [];
+  let hasLegacyState = false;
+  try {
+    hasLegacyState = await fileSystemService.exists(legacyStatePath);
+  } catch (err) {
+    legacyProbeFailures.push({
+      path: legacyStatePath,
+      reason: `Could not inspect legacy project setup marker: ${err instanceof Error ? err.message : String(err)}`
+    });
+  }
+  const hasWork = configured.length > 0 || hasLegacyState;
+  if (!hasWork && failedChecks.length === 0 && legacyProbeFailures.length === 0) {
+    printProjectUninstallSummary({
+      removed: [],
+      legacyRemoved: [],
+      skipped,
+      failed: []
+    });
+    return;
+  }
+  if (!hasWork) {
+    const summary2 = {
+      removed: [],
+      legacyRemoved: [],
+      skipped,
+      failed: failedChecks.map(({ setup, check }) => ({
+        path: setup.configPath,
+        reason: check.message
+      })).concat(legacyProbeFailures)
+    };
+    process.exitCode = 1;
+    printProjectUninstallSummary(summary2);
+    return;
+  }
+  if (!isInteractive && !options.yes) {
+    console.log("  Project uninstall needs confirmation. Because this session is non-interactive, no changes were made.");
+    console.log();
+    console.log("  To remove GitHits from this project's MCP files, run:");
+    console.log(`    ${formatCommand("githits init uninstall --project --yes", useColors)}`);
+    console.log();
+    return;
+  }
+  if (!options.yes) {
+    let accepted;
+    try {
+      accepted = await promptService.confirm("Remove GitHits MCP config from this project?", false);
+    } catch (err) {
+      if (err instanceof ExitPromptError) {
+        console.log(`
+  Uninstall cancelled. No changes made.
+`);
+        return;
+      }
+      throw err;
+    }
+    if (!accepted) {
+      printTask("skipped", "Project uninstall skipped", "no changes made", useColors);
+      console.log();
+      return;
+    }
+  }
+  const summary = {
+    removed: [],
+    legacyRemoved: [],
+    skipped,
+    failed: failedChecks.map(({ setup, check }) => ({
+      path: setup.configPath,
+      reason: check.message
+    })).concat(legacyProbeFailures)
+  };
+  for (const { setup } of configured) {
+    const result = await executeConfigFileUninstall(setup, fileSystemService);
+    if (result.status === "removed") {
+      summary.removed.push(setup.configPath);
+      printTask("success", "GitHits project config", `removed from ${setup.configPath}`, useColors);
+    } else if (result.status === "not_configured") {
+      summary.skipped.push(setup.configPath);
+      printTask("skipped", setup.configPath, "not configured", useColors);
+    } else {
+      summary.failed.push({
+        path: setup.configPath,
+        reason: result.message
+      });
+      printTask("failed", setup.configPath, result.message, useColors);
+    }
+  }
+  if (legacyProbeFailures.length === 0) {
+    const legacyCleanup = await cleanupLegacyProjectSetupState(fileSystemService);
+    for (const path of legacyCleanup.removed) {
+      summary.legacyRemoved.push(path);
+      printTask("success", "Legacy project setup marker", `removed ${path}`, useColors);
+    }
+    for (const failure of legacyCleanup.failed) {
+      summary.failed.push(failure);
+      printTask("failed", failure.path, failure.reason, useColors);
+    }
+  }
+  if (summary.failed.length > 0) {
+    process.exitCode = 1;
+  }
+  printProjectUninstallSummary(summary);
+}
+function printNonInteractiveUninstallGuidance(useColors) {
+  console.log("  Uninstall is interactive. Because this session is non-interactive, no changes were made.");
+  console.log();
+  console.log("  To remove user-level GitHits MCP config, run:");
+  console.log(`    ${formatCommand("githits init uninstall --yes", useColors)}`);
+  console.log();
+  console.log("  To remove project-level GitHits MCP config, run:");
+  console.log(`    ${formatCommand("githits init uninstall --project --yes", useColors)}`);
+  console.log();
+}
+async function runUserMcpUninstall(options, deps, useColors) {
+  const { fileSystemService, promptService, execService } = deps;
+  console.log(`
+  ${colorize("Disconnect GitHits from your coding agents.", "bold", useColors)}`);
+  console.log(`  ${colorize("Removes the local GitHits MCP configuration.", "dim", useColors)}
+`);
+  console.log(`  Scanning for configured agents...
+`);
+  const scan = await scanAgentsForUninstall(fileSystemService, execService);
+  for (const agent of scan.configured) {
+    console.log(`    ${colorize(`● ${agent.name} — configured`, "cyan", useColors)}`);
+  }
+  for (const agent of scan.notConfigured) {
+    console.log(`    ${warning(`${agent.name} — not configured`, useColors)}`);
+  }
+  for (const outcome of scan.failed) {
+    console.log(`    ${error(`${outcome.name} — cannot inspect config`, useColors)}`);
+  }
+  for (const agent of scan.notDetected) {
+    console.log(`    ${colorize(`${agent.name} — not detected`, "dim", useColors)}`);
+  }
+  console.log();
+  if (scan.configured.length === 0 && scan.failed.length === 0) {
+    console.log(`  No GitHits MCP configurations found. Nothing to uninstall.
+`);
+    return;
+  }
+  const outcomes = [...scan.failed];
+  let alwaysMode = options.yes ?? false;
+  for (const agent of scan.configured) {
+    console.log(`  Uninstalling from ${colorize(agent.name, "bold", useColors)}...
+`);
+    const setupConfig = getResolvedSetupConfig(agent, fileSystemService);
+    const uninstallConfig = agent.resolvedUninstallConfig ?? (setupConfig.method === "config-file" ? setupConfig : agent.getUninstallConfig?.(fileSystemService, agent.resolvedSetupContext));
+    if (!uninstallConfig) {
+      outcomes.push({
+        id: agent.id,
+        name: agent.name,
+        status: "failed",
+        message: `${agent.name} does not have a verified uninstall command.`
+      });
+      console.log(`    ${error(`${agent.name} does not have a verified uninstall command.`, useColors)}
+`);
+      continue;
+    }
+    const preview2 = formatUninstallPreview(uninstallConfig);
+    for (const line of preview2.split(`
+`)) {
+      console.log(`    ${line}`);
+    }
+    console.log();
+    if (!alwaysMode) {
+      let choice;
+      try {
+        choice = await promptService.confirm3("Proceed?", "no");
+      } catch (err) {
+        if (err instanceof ExitPromptError) {
+          console.log(`
+  Uninstall cancelled.
+`);
+          return;
+        }
+        throw err;
+      }
+      if (choice === "no") {
+        outcomes.push({ id: agent.id, name: agent.name, status: "skipped" });
+        console.log();
+        continue;
+      }
+      if (choice === "always") {
+        alwaysMode = true;
+      }
+    }
+    let result = uninstallConfig.method === "cli" ? await executeCliUninstall(uninstallConfig, execService) : uninstallConfig.method === "config-file" ? await executeConfigFileUninstall(uninstallConfig, fileSystemService) : await executeCompositeUninstall(uninstallConfig, fileSystemService, execService);
+    if (result.status === "removed" && !agent.skipUninstallVerification) {
+      const verification = await verifyAgentUnconfigured(agent, fileSystemService, execService);
+      if (!verification.ok) {
+        result = {
+          status: "failed",
+          message: verification.message ?? `${agent.name} verification failed after uninstall.`,
+          warnings: result.warnings
+        };
+      }
+    }
+    outcomes.push({
+      id: agent.id,
+      name: agent.name,
+      status: result.status,
+      message: result.status === "failed" ? result.message : undefined,
+      warnings: result.warnings
+    });
+    if (result.status === "removed") {
+      console.log(`    ${success(`${agent.name} removed`, useColors)}
+`);
+      for (const warn of result.warnings ?? []) {
+        console.log(`    ${warning(`Warning: ${warn}`, useColors)}`);
+      }
+    } else if (result.status === "not_configured") {
+      console.log(`    ${warning(`${agent.name} was not configured`, useColors)}
+`);
+    } else {
+      console.log(`    ${error(result.message, useColors)}
+`);
+      for (const warn of result.warnings ?? []) {
+        console.log(`    ${warning(`Warning: ${warn}`, useColors)}`);
+      }
+    }
+  }
+  const removed = outcomes.filter((o) => o.status === "removed").length;
+  const notConfigured = outcomes.filter((o) => o.status === "not_configured").length + scan.notConfigured.length;
+  const failed = outcomes.filter((o) => o.status === "failed").length;
+  const skipped = outcomes.filter((o) => o.status === "skipped").length;
+  if (failed > 0) {
+    console.log("  Uninstall completed with errors.");
+  } else if (removed > 0) {
+    console.log("  Done! GitHits MCP configuration was removed.");
+  } else if (skipped > 0) {
+    console.log("  Uninstall skipped.");
+  } else if (notConfigured > 0) {
+    console.log("  No GitHits MCP configurations were active. Nothing to remove.");
+  }
+  if (removed > 0) {
+    console.log(`  ${removed} agent${removed !== 1 ? "s" : ""} removed.`);
+  }
+  if (notConfigured > 0) {
+    console.log(`  ${notConfigured} agent${notConfigured !== 1 ? "s" : ""} not configured.`);
+  }
+  if (skipped > 0) {
+    console.log(`  ${skipped} agent${skipped !== 1 ? "s" : ""} skipped.`);
+  }
+  if (failed > 0) {
+    console.log(`  ${failed} agent${failed !== 1 ? "s" : ""} failed to uninstall.`);
+    for (const outcome of outcomes.filter((o) => o.status === "failed")) {
+      console.log(`    - ${outcome.name}: ${outcome.message ?? "Unknown error"}`);
+      for (const warn of outcome.warnings ?? []) {
+        console.log(`      Warning: ${warn}`);
+      }
+    }
+  }
+  console.log();
+}
+async function verifyAgentConfigured(agent, fileSystemService, execService, scope) {
+  const postCheck = await scanAgents([agent], fileSystemService, execService, {
+    scope
+  });
+  if (postCheck.alreadyConfigured.some((a) => a.id === agent.id)) {
+    return { ok: true };
+  }
+  if (postCheck.needsSetup.some((a) => a.id === agent.id)) {
+    return {
+      ok: false,
+      message: `${agent.name} verification failed: not configured after setup.`
+    };
+  }
+  return {
+    ok: false,
+    message: `${agent.name} verification failed: agent not detected after setup.`
+  };
+}
+async function executeAgentSetupWithVerification(agent, fileSystemService, execService, scope) {
+  const config = getResolvedSetupConfig(agent, fileSystemService);
+  let result = config.method === "cli" ? await executeCliSetup(config, execService) : config.method === "config-file" ? await executeConfigFileSetup(config, fileSystemService) : await executeCompositeSetup(config, fileSystemService, execService);
+  if (result.status === "success" || result.status === "already_configured") {
+    const verification = await verifyAgentConfigured(agent, fileSystemService, execService, scope);
+    if (!verification.ok) {
+      result = {
+        status: "failed",
+        message: agent.id === "gemini-cli" ? "Gemini installation did not complete. Retry, or run: gemini extensions install --consent https://github.com/githits-com/githits-cli" : verification.message ?? `${agent.name} verification failed after setup.`
+      };
+    }
+  }
+  return result;
+}
+async function installSelectedAgents(agents, scan, fileSystemService, execService, useColors, printResults, scope = "user") {
+  const alreadyConfiguredIds = new Set(scan.alreadyConfigured.map((agent) => agent.id));
+  const outcomes = [];
+  const installTasks = createInstallTaskReporter(useColors);
+  for (const agent of agents) {
+    if (alreadyConfiguredIds.has(agent.id)) {
+      outcomes.push({
+        id: agent.id,
+        name: agent.name,
+        status: "already_configured"
+      });
+      if (printResults) {
+        printTask("warning", agent.name, "already configured", useColors);
+      }
+      continue;
+    }
+    const finishTask = printResults ? installTasks.start(agent.name) : () => {};
+    let result;
+    try {
+      result = await executeAgentSetupWithVerification(agent, fileSystemService, execService, scope);
+    } finally {
+      finishTask();
+    }
+    outcomes.push({
+      id: agent.id,
+      name: agent.name,
+      status: result.status,
+      message: result.status === "failed" ? result.message : undefined
+    });
+    if (!printResults) {
       continue;
     }
     if (result.status === "success") {
@@ -11568,6 +12317,7 @@ async function initAction(options, deps) {
     console.log();
     return;
   }
+  let setupScope = options.project ? "project" : "user";
   if (!options.yes) {
     let intent;
     try {
@@ -11589,20 +12339,39 @@ async function initAction(options, deps) {
       console.log("\n  No changes made. Run `npx githits@latest init` whenever you're ready.\n");
       return;
     }
+    if (!options.project) {
+      try {
+        setupScope = await promptService.select("  Where should GitHits be configured?", INIT_SCOPE_CHOICES, "user");
+      } catch (err) {
+        if (err instanceof ExitPromptError) {
+          console.log(`
+  Setup cancelled. No changes made.
+`);
+          return;
+        }
+        throw err;
+      }
+    }
+  }
+  if (setupScope === "project") {
+    const scope = await resolveProjectSetupScope({}, fileSystemService);
+    if (!scope)
+      return;
+    printProjectScopeExplanation(useColors);
   }
   printSection(1, "Detect tools", useColors);
   console.log("    Scanning for compatible AI coding tools...");
   const progress = createScanProgressReporter(useColors);
-  const scanPromise = startSafeInitScan(fileSystemService, execService, (scanProgress) => progress.onProgress(scanProgress));
+  const scanPromise = startSafeInitScan(fileSystemService, execService, setupScope, (scanProgress) => progress.onProgress(scanProgress));
   let scan;
   try {
     scan = await unwrapSafeScan(scanPromise);
   } finally {
     progress.finish();
   }
-  printScanSummary(scan, useColors);
+  printScanSummary(scan, useColors, setupScope);
   if (scan.needsSetup.length === 0 && scan.alreadyConfigured.length === 0) {
-    printTask("warning", "No supported AI coding tools detected", "install a supported tool and run `githits init` again", useColors);
+    printTask("warning", setupScope === "project" ? "No project-configurable tools detected" : "No supported AI coding tools detected", setupScope === "project" ? "choose user-level config or install a project-configurable tool" : "install a supported tool and run `githits init` again", useColors);
     console.log();
     return;
   }
@@ -11630,6 +12399,9 @@ async function initAction(options, deps) {
     console.log();
     return;
   }
+  if (toSetup.length > 0) {
+    await printTomlRewriteWarnings(toSetup, fileSystemService, useColors);
+  }
   printSection(3, "Sign in", useColors);
   const authStatus = await runInitAuthentication(options, promptService, createLoginDeps, useColors);
   if (authStatus === "cancelled") {
@@ -11638,11 +12410,11 @@ async function initAction(options, deps) {
   printSection(4, "Install and verify", useColors);
   if (toSetup.length === 0) {
     printTask("success", "Nothing to install", "all detected tools are already configured", useColors);
-    printPostSetupNextSteps(authStatus, useColors);
+    printScopedNextSteps(setupScope, authStatus, useColors);
     console.log();
     return;
   }
-  const outcomes = await installSelectedAgents(toSetup, scan, fileSystemService, execService, useColors, true);
+  const outcomes = await installSelectedAgents(toSetup, scan, fileSystemService, execService, useColors, true, setupScope);
   console.log();
   const configured = outcomes.filter((o) => o.status === "success").length;
   const alreadyDone = outcomes.filter((o) => o.status === "already_configured").length + scan.alreadyConfigured.length;
@@ -11650,7 +12422,7 @@ async function initAction(options, deps) {
   if (failed > 0) {
     console.log("  Setup completed with errors.");
   } else if (configured > 0 || alreadyDone > 0) {
-    printPostSetupNextSteps(authStatus, useColors);
+    printScopedNextSteps(setupScope, authStatus, useColors);
   }
   if (failed > 0) {
     console.log(`  ${failed} tool${failed !== 1 ? "s" : ""} failed to configure.`);
@@ -11665,145 +12437,35 @@ async function initAction(options, deps) {
 }
 async function initUninstallAction(options, deps) {
   const useColors = shouldUseColors();
-  const { fileSystemService, promptService, execService } = deps;
-  console.log(`
-  ${colorize("Disconnect GitHits from your coding agents.", "bold", useColors)}`);
-  console.log(`  ${colorize("Removes the local GitHits MCP configuration.", "dim", useColors)}
-`);
-  console.log(`  Scanning for configured agents...
-`);
-  const scan = await scanAgentsForUninstall(fileSystemService, execService);
-  for (const agent of scan.configured) {
-    console.log(`    ${colorize(`● ${agent.name} — configured`, "cyan", useColors)}`);
-  }
-  for (const agent of scan.notConfigured) {
-    console.log(`    ${warning(`${agent.name} — not configured`, useColors)}`);
-  }
-  for (const outcome of scan.failed) {
-    console.log(`    ${error(`${outcome.name} — cannot inspect config`, useColors)}`);
-  }
-  for (const agent of scan.notDetected) {
-    console.log(`    ${colorize(`${agent.name} — not detected`, "dim", useColors)}`);
+  const { promptService } = deps;
+  const isInteractive = deps.isInteractive ?? true;
+  if (options.project) {
+    await runProjectMcpUninstall(options, deps, useColors);
+    return;
   }
-  console.log();
-  if (scan.configured.length === 0 && scan.failed.length === 0) {
-    console.log(`  No GitHits MCP configurations found. Nothing to uninstall.
-`);
+  if (!isInteractive && !options.yes) {
+    printNonInteractiveUninstallGuidance(useColors);
     return;
   }
-  const outcomes = [...scan.failed];
-  let alwaysMode = options.yes ?? false;
-  for (const agent of scan.configured) {
-    console.log(`  Uninstalling from ${colorize(agent.name, "bold", useColors)}...
-`);
-    const setupConfig = getResolvedSetupConfig(agent, fileSystemService);
-    const uninstallConfig = agent.resolvedUninstallConfig ?? (setupConfig.method === "config-file" ? setupConfig : agent.getUninstallConfig?.(fileSystemService, agent.resolvedSetupContext));
-    if (!uninstallConfig) {
-      outcomes.push({
-        id: agent.id,
-        name: agent.name,
-        status: "failed",
-        message: `${agent.name} does not have a verified uninstall command.`
-      });
-      console.log(`    ${error(`${agent.name} does not have a verified uninstall command.`, useColors)}
-`);
-      continue;
-    }
-    const preview2 = formatUninstallPreview(uninstallConfig);
-    for (const line of preview2.split(`
-`)) {
-      console.log(`    ${line}`);
-    }
-    console.log();
-    if (!alwaysMode) {
-      let choice;
-      try {
-        choice = await promptService.confirm3("Proceed?");
-      } catch (err) {
-        if (err instanceof ExitPromptError) {
-          console.log(`
-  Uninstall cancelled.
-`);
-          return;
-        }
-        throw err;
-      }
-      if (choice === "no") {
-        outcomes.push({ id: agent.id, name: agent.name, status: "skipped" });
-        console.log();
-        continue;
-      }
-      if (choice === "always") {
-        alwaysMode = true;
-      }
-    }
-    let result = uninstallConfig.method === "cli" ? await executeCliUninstall(uninstallConfig, execService) : uninstallConfig.method === "config-file" ? await executeConfigFileUninstall(uninstallConfig, fileSystemService) : await executeCompositeUninstall(uninstallConfig, fileSystemService, execService);
-    if (result.status === "removed" && !agent.skipUninstallVerification) {
-      const verification = await verifyAgentUnconfigured(agent, fileSystemService, execService);
-      if (!verification.ok) {
-        result = {
-          status: "failed",
-          message: verification.message ?? `${agent.name} verification failed after uninstall.`,
-          warnings: result.warnings
-        };
-      }
-    }
-    outcomes.push({
-      id: agent.id,
-      name: agent.name,
-      status: result.status,
-      message: result.status === "failed" ? result.message : undefined,
-      warnings: result.warnings
-    });
-    if (result.status === "removed") {
-      console.log(`    ${success(`${agent.name} removed`, useColors)}
-`);
-      for (const warn of result.warnings ?? []) {
-        console.log(`    ${warning(`Warning: ${warn}`, useColors)}`);
-      }
-    } else if (result.status === "not_configured") {
-      console.log(`    ${warning(`${agent.name} was not configured`, useColors)}
-`);
-    } else {
-      console.log(`    ${error(result.message, useColors)}
+  if (!options.yes) {
+    let scope;
+    try {
+      scope = await promptService.select("  What should GitHits be removed from?", INIT_UNINSTALL_SCOPE_CHOICES, "user");
+    } catch (err) {
+      if (err instanceof ExitPromptError) {
+        console.log(`
+  Uninstall cancelled. No changes made.
 `);
-      for (const warn of result.warnings ?? []) {
-        console.log(`    ${warning(`Warning: ${warn}`, useColors)}`);
+        return;
       }
+      throw err;
     }
-  }
-  const removed = outcomes.filter((o) => o.status === "removed").length;
-  const notConfigured = outcomes.filter((o) => o.status === "not_configured").length + scan.notConfigured.length;
-  const failed = outcomes.filter((o) => o.status === "failed").length;
-  const skipped = outcomes.filter((o) => o.status === "skipped").length;
-  if (failed > 0) {
-    console.log("  Uninstall completed with errors.");
-  } else if (removed > 0) {
-    console.log("  Done! GitHits MCP configuration was removed.");
-  } else if (skipped > 0) {
-    console.log("  Uninstall skipped.");
-  } else if (notConfigured > 0) {
-    console.log("  No GitHits MCP configurations were active. Nothing to remove.");
-  }
-  if (removed > 0) {
-    console.log(`  ${removed} agent${removed !== 1 ? "s" : ""} removed.`);
-  }
-  if (notConfigured > 0) {
-    console.log(`  ${notConfigured} agent${notConfigured !== 1 ? "s" : ""} not configured.`);
-  }
-  if (skipped > 0) {
-    console.log(`  ${skipped} agent${skipped !== 1 ? "s" : ""} skipped.`);
-  }
-  if (failed > 0) {
-    console.log(`  ${failed} agent${failed !== 1 ? "s" : ""} failed to uninstall.`);
-    for (const outcome of outcomes.filter((o) => o.status === "failed")) {
-      console.log(`    - ${outcome.name}: ${outcome.message ?? "Unknown error"}`);
-      for (const warn of outcome.warnings ?? []) {
-        console.log(`      Warning: ${warn}`);
-      }
+    if (scope === "project") {
+      await runProjectMcpUninstall(options, deps, useColors);
+      return;
     }
   }
-  console.log();
+  await runUserMcpUninstall(options, deps, useColors);
 }
 function printAuthRecoveryHint(useColors) {
   console.log("    You can still configure MCP, but GitHits tools will require auth.");
@@ -11821,30 +12483,45 @@ sets up Agent Skills instead. Detects supported coding tools on this machine,
 signs you in, and configures the tools you select.`;
 var INIT_UNINSTALL_DESCRIPTION = `Remove GitHits MCP server configuration from your coding agents.
 
-Scans for available agents that currently have GitHits configured, then removes
-only the GitHits MCP/plugin configuration with your confirmation. Authentication
-tokens are not removed; use \`githits logout\` to remove stored credentials.`;
+In interactive mode, asks whether to remove user-level coding-agent config or
+project-level MCP config. Removes only GitHits MCP/plugin entries with your
+confirmation. Authentication tokens are not removed; use \`githits logout\` to
+remove stored credentials.`;
 function registerInitCommand(program) {
-  const initCommand = program.command("init").summary("Connect GitHits to your coding agents").description(INIT_DESCRIPTION).option("-y, --yes", "Skip prompts, configure all detected tools").option("--skip-login", "Skip authentication step").option("--detect-agents", "Scan supported agents without installing").option("--install-agents <ids>", "Install MCP server for comma-separated agent IDs from --detect-agents").option("--json", "Emit JSON for --detect-agents or --install-agents").action(async (options) => {
+  const initCommand = program.command("init").argument("[action]", "Compatibility action; use uninstall with --project").summary("Connect GitHits to your coding agents").description(INIT_DESCRIPTION).option("-y, --yes", "Skip prompts, configure all detected tools").option("--skip-login", "Skip authentication step").option("--project", "Configure project-level MCP in the current directory").option("--detect-agents", "Scan supported agents without installing").option("--install-agents <ids>", "Install MCP server for comma-separated agent IDs from --detect-agents").option("--json", "Emit JSON for --detect-agents or --install-agents").action(async (action, options) => {
     const fileSystemService = new FileSystemServiceImpl;
     const promptService = new PromptServiceImpl;
     const execService = new ExecServiceImpl;
-    await initAction(options, {
+    const deps = {
       fileSystemService,
       promptService,
       execService,
       createLoginDeps: () => createContainer(),
       isInteractive: process.stdin.isTTY === true && process.stdout.isTTY === true
+    };
+    if (action !== undefined) {
+      failUnknownInitAction(action);
+      return;
+    }
+    await initAction(options, {
+      ...deps
     });
   });
-  initCommand.command("uninstall").summary("Remove MCP server from your coding agents").description(INIT_UNINSTALL_DESCRIPTION).option("-y, --yes", "Skip prompts, uninstall from all configured agents").action(async (options) => {
+  initCommand.command("uninstall").summary("Remove MCP server from coding agents or project config").description(INIT_UNINSTALL_DESCRIPTION).option("-y, --yes", "Skip prompts, uninstall user-level config", false).option("--project", "Remove project-level MCP from the current directory", false).action(async (options, command) => {
+    const parentOptions = command.parent?.opts() ?? {};
+    const resolvedOptions = {
+      ...options,
+      yes: options.yes || parentOptions.yes,
+      project: options.project || parentOptions.project
+    };
     const fileSystemService = new FileSystemServiceImpl;
     const promptService = new PromptServiceImpl;
     const execService = new ExecServiceImpl;
-    await initUninstallAction(options, {
+    await initUninstallAction(resolvedOptions, {
       fileSystemService,
       promptService,
-      execService
+      execService,
+      isInteractive: process.stdin.isTTY === true && process.stdout.isTTY === true
     });
   });
 }
@@ -12088,8 +12765,13 @@ function resolveCodeTarget(target) {
       return mappedInvalidTargetResult(error2);
     }
   }
-  const hasPackageTarget = Boolean(target.registry || target.package_name);
-  const hasRepoTarget = Boolean(target.repo_url || target.git_ref);
+  const registry = normaliseOptionalValue(target.registry)?.toLowerCase();
+  const packageName = normaliseOptionalValue(target.package_name);
+  const version2 = normaliseOptionalValue(target.version);
+  const repoUrl = normaliseOptionalValue(target.repo_url);
+  const gitRef = normaliseOptionalValue(target.git_ref);
+  const hasPackageTarget = registry !== undefined || packageName !== undefined;
+  const hasRepoTarget = repoUrl !== undefined || gitRef !== undefined;
   if (hasPackageTarget && hasRepoTarget) {
     return invalidTargetResult("Invalid target: provide either registry + package_name or repo_url with optional git_ref, not both.");
   }
@@ -12097,23 +12779,29 @@ function resolveCodeTarget(target) {
     return invalidTargetResult("Missing target: provide registry + package_name or repo_url.");
   }
   if (hasPackageTarget) {
-    if (!target.registry || !target.package_name) {
+    if (!registry || !packageName) {
       return invalidTargetResult("Incomplete package target: both registry and package_name are required.");
     }
     return {
-      registry: toCodeNavigationRegistry(target.registry),
-      packageName: target.package_name,
-      version: target.version
+      registry: toCodeNavigationRegistry(registry),
+      packageName,
+      version: version2
     };
   }
-  if (!target.repo_url) {
+  if (!repoUrl) {
     return invalidTargetResult("Incomplete repository target: repo_url is required.");
   }
   return {
-    repoUrl: target.repo_url,
-    gitRef: target.git_ref
+    repoUrl,
+    gitRef
   };
 }
+function normaliseOptionalValue(value) {
+  if (value === undefined)
+    return;
+  const trimmed = value.trim();
+  return trimmed.length > 0 ? trimmed : undefined;
+}
 function mappedInvalidTargetResult(error2) {
   const mapped = mapCodeNavigationError(error2);
   return errorResult(JSON.stringify({
@@ -12410,7 +13098,7 @@ function buildPackageChangelogParams(input) {
   };
 }
 function resolveAddressing(input) {
-  const hasSpec = Boolean(input.registry || input.packageName);
+  const hasSpec = hasNonBlankValue2(input.registry) || hasNonBlankValue2(input.packageName);
   const hasRepoUrl = Boolean(input.repoUrl?.trim());
   if (hasSpec && hasRepoUrl) {
     throw new InvalidPackageSpecError("Provide either `<spec>` (registry + name) or `--repo-url` / `repo_url`, not both.");
@@ -12436,6 +13124,9 @@ function resolveAddressing(input) {
   const registry = toPkgseerRegistry(normalisedRegistryArg);
   return { registry, packageName };
 }
+function hasNonBlankValue2(value) {
+  return value !== undefined && value.trim().length > 0;
+}
 function normaliseGitRef(raw) {
   if (raw === undefined)
     return;
@@ -13247,11 +13938,13 @@ function createSearchTool(service) {
     annotations: { readOnlyHint: true },
     handler: async (args) => {
       try {
-        const resolvedTarget = args.target ? resolveSearchTarget(args.target) : undefined;
+        const effectiveTarget = isBlankSearchTarget(args.target) ? undefined : args.target;
+        const resolvedTarget = effectiveTarget ? resolveSearchTarget(effectiveTarget) : undefined;
         if (resolvedTarget && "content" in resolvedTarget)
           return resolvedTarget;
-        const effectiveTargets = args.targets?.length ? args.targets : undefined;
-        const resolvedTargets = effectiveTargets?.map((entry) => resolveSearchTarget(entry));
+        const effectiveTargets = args.targets?.filter((target) => !isBlankSearchTarget(target));
+        const nonEmptyTargets = effectiveTargets?.length ? effectiveTargets : undefined;
+        const resolvedTargets = nonEmptyTargets?.map((entry) => resolveSearchTarget(entry));
         const resolvedTargetsError = resolvedTargets?.find((entry) => ("content" in entry));
         if (resolvedTargetsError) {
           return resolvedTargetsError;
@@ -13289,6 +13982,19 @@ function createSearchTool(service) {
     }
   };
 }
+function isBlankSearchTarget(target) {
+  if (target === undefined)
+    return true;
+  if (typeof target === "string")
+    return target.trim().length === 0;
+  return !(normaliseOptionalValue2(target.registry) || normaliseOptionalValue2(target.package_name) || normaliseOptionalValue2(target.version) || normaliseOptionalValue2(target.repo_url) || normaliseOptionalValue2(target.git_ref));
+}
+function normaliseOptionalValue2(value) {
+  if (value === undefined)
+    return;
+  const trimmed = value.trim();
+  return trimmed.length > 0 ? trimmed : undefined;
+}
 function isResolvedSearchTarget(target) {
   return !("content" in target);
 }
@@ -13306,8 +14012,13 @@ function resolveSearchTarget(target) {
       }));
     }
   }
-  const hasPackageTarget = Boolean(target.registry || target.package_name);
-  const hasRepoTarget = Boolean(target.repo_url || target.git_ref);
+  const registry = normaliseOptionalValue2(target.registry)?.toLowerCase();
+  const packageName = normaliseOptionalValue2(target.package_name);
+  const version2 = normaliseOptionalValue2(target.version);
+  const repoUrl = normaliseOptionalValue2(target.repo_url);
+  const gitRef = normaliseOptionalValue2(target.git_ref);
+  const hasPackageTarget = registry !== undefined || packageName !== undefined;
+  const hasRepoTarget = repoUrl !== undefined || gitRef !== undefined;
   if (hasPackageTarget && hasRepoTarget) {
     return invalidSearchTargetResult("Invalid target: provide either registry + package_name or repo_url with optional git_ref, not both.");
   }
@@ -13315,19 +14026,19 @@ function resolveSearchTarget(target) {
     return invalidSearchTargetResult("Missing target: provide registry + package_name or repo_url.");
   }
   if (hasPackageTarget) {
-    if (!target.registry || !target.package_name) {
+    if (!registry || !packageName) {
       return invalidSearchTargetResult("Incomplete package target: both registry and package_name are required.");
     }
     return {
-      registry: toCodeNavigationRegistry(target.registry),
-      packageName: target.package_name,
-      version: target.version
+      registry: toCodeNavigationRegistry(registry),
+      packageName,
+      version: version2
     };
   }
-  if (!target.repo_url) {
+  if (!repoUrl) {
     return invalidSearchTargetResult("Incomplete repository target: repo_url is required.");
   }
-  return { repoUrl: target.repo_url, gitRef: target.git_ref };
+  return { repoUrl, gitRef };
 }
 function invalidSearchTargetResult(message) {
   return errorResult(JSON.stringify({
@@ -14292,7 +15003,7 @@ function requireSearchService(deps) {
   return deps.codeNavigationService;
 }
 async function loadContainer2() {
-  const { createContainer: createContainer2 } = await import("./shared/chunk-mw1910qd.js");
+  const { createContainer: createContainer2 } = await import("./shared/chunk-2w48kb4c.js");
   return createContainer2();
 }
 function parseTargetSpecs(specs) {