feat(mcp): unified MCP registry, source-aware mcp_query, and doctor adoption#22
feat(mcp): unified MCP registry, source-aware mcp_query, and doctor adoption#22codewithkenzo wants to merge 25 commits intodevfrom
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- state.test.ts: enable getMainSessionID undefined test (was skipped due to state pollution) - ralph-loop/index.test.ts: enable timeout protection test (reduced delay from 10s to 200ms) - state.ts: add clearMainSession export for test isolation
- Add console.error logging to stderr read error handler - Add console.error logging to JSON parse error handler - Add debug logging for /proc/version read failure Closes: audit-2026-02-01
- Define proper TuiClient interface instead of 'as any' type assertion - Replace empty catch blocks with error logging - Improve type safety and debugging visibility
- Add MessageInfo and ThinkingPart interfaces - Replace as any casts with proper type assertions - Improves TypeScript strictness and code maintainability
Rebased Sprint 1 (agent compression 23→8) and Sprint 2 (skill system modernization) onto current main branch, integrating memory-persistence hooks, research tools, type safety fixes, and other main-branch additions. Key changes: - Agent compression: 23 agents → 8 with LEGACY_TO_MUSASHI_NAME compat map - Skill system: split 1204-line skills.ts into per-skill files - BrowserAutomationProvider config + agent-browser/dev-browser skills - Atlas hook (renamed from sisyphus-orchestrator) with BackgroundManager - Per-provider skill cache in skill-content.ts - Added case-insensitive utilities and model availability modules
…luginConfigToClaudeConfig
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| import { createMcpRegistry, filterMcpRegistryServers } from "../../../features/mcp-registry" | ||
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| const BUILTIN_MCP_SERVERS = ["context7", "grep_app"] | ||
| export async function getBuiltinMcpInfo(): Promise<McpServerInfo[]> { | ||
| const registry = createMcpRegistry({ | ||
| builtinServers: createBuiltinMcps(), | ||
| }) | ||
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| const MCP_CONFIG_PATHS = [ | ||
| join(homedir(), ".claude", ".mcp.json"), | ||
| join(process.cwd(), ".mcp.json"), | ||
| join(process.cwd(), ".claude", ".mcp.json"), | ||
| ] | ||
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| interface McpConfig { | ||
| mcpServers?: Record<string, unknown> | ||
| } | ||
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| function loadUserMcpConfig(): Record<string, unknown> { | ||
| const servers: Record<string, unknown> = {} | ||
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| for (const configPath of MCP_CONFIG_PATHS) { | ||
| if (!existsSync(configPath)) continue | ||
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| try { | ||
| const content = readFileSync(configPath, "utf-8") | ||
| const config = parseJsonc<McpConfig>(content) | ||
| if (config.mcpServers) { | ||
| Object.assign(servers, config.mcpServers) | ||
| } | ||
| } catch { | ||
| // intentionally empty - skip invalid configs | ||
| } | ||
| } | ||
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| return servers | ||
| } | ||
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| export function getBuiltinMcpInfo(): McpServerInfo[] { | ||
| return BUILTIN_MCP_SERVERS.map((id) => ({ | ||
| id, | ||
| return filterMcpRegistryServers(registry, "builtin").map((server) => ({ | ||
| id: server.name, | ||
| type: "builtin" as const, | ||
| enabled: true, |
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User MCP validity lost
getUserMcpInfo() now returns every custom MCP as { valid: true } and no longer attempts to validate/flag malformed entries. Previously, invalid mcpServers entries were surfaced as valid: false with an error. With this change, doctor can report a “healthy” config even when .mcp.json contains invalid shapes, which is a regression in the check’s purpose.
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Path: src/cli/doctor/checks/mcp.ts
Line: 5:15
Comment:
**User MCP validity lost**
`getUserMcpInfo()` now returns every custom MCP as `{ valid: true }` and no longer attempts to validate/flag malformed entries. Previously, invalid `mcpServers` entries were surfaced as `valid: false` with an error. With this change, `doctor` can report a “healthy” config even when `.mcp.json` contains invalid shapes, which is a regression in the check’s purpose.
How can I resolve this? If you propose a fix, please make it concise.| @@ -282,10 +341,8 @@ export function createConfigHandler(deps: ConfigHandlerDeps) { | |||
| ...projectAgents, | |||
| ...pluginAgents, | |||
| ...filteredConfigAgents, | |||
| build: { ...migratedBuild, mode: "subagent", hidden: true, disable: true }, | |||
| build: { ...migratedBuild, mode: "subagent", hidden: true }, | |||
| ...(planDemoteConfig ? { plan: planDemoteConfig } : {}), | |||
| explore: { disable: true }, | |||
| general: { disable: true }, | |||
| }; | |||
| } else { | |||
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Demoted agents still enabled
When replacePlan is true, the code used to demote/disable OpenCode’s plan agent via { hidden: true, disable: true }, but now sets only { mode: "subagent" } (and similarly removed disable: true for build). This makes the “demoted” agents still selectable/usable by OpenCode, which changes behavior and can lead to the defaults competing with your intended builtins (and the PR comment suggests you’re trying to prevent overwrites).
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Path: src/plugin-handlers/config-handler.ts
Line: 329:347
Comment:
**Demoted agents still enabled**
When `replacePlan` is true, the code used to demote/disable OpenCode’s `plan` agent via `{ hidden: true, disable: true }`, but now sets only `{ mode: "subagent" }` (and similarly removed `disable: true` for `build`). This makes the “demoted” agents still selectable/usable by OpenCode, which changes behavior and can lead to the defaults competing with your intended builtins (and the PR comment suggests you’re trying to prevent overwrites).
How can I resolve this? If you propose a fix, please make it concise.| delegate_task: "deny", | ||
| }; | ||
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| const mcpResult = (pluginConfig.claude_code?.mcp ?? true) | ||
| ? await loadMcpConfigs() | ||
| : { servers: {} }; | ||
| const includeCustomMcp = pluginConfig.claude_code?.mcp ?? true; | ||
| const customRawServers = includeCustomMcp | ||
| ? (await loadRawMcpConfigs()).loadedServers | ||
| : []; | ||
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| const mcpRegistry = createMcpRegistry({ | ||
| builtinServers: createBuiltinMcps(pluginConfig.disabled_mcps), | ||
| customServers: customRawServers, | ||
| pluginServers: pluginComponents.mcpServers, | ||
| }); | ||
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| if (mcpRegistry.collisions.length > 0) { | ||
| log("MCP registry collisions detected", { | ||
| collisions: mcpRegistry.collisions.map((entry) => ({ | ||
| name: entry.name, | ||
| winner: `${entry.winner.source}:${entry.winner.scope}`, | ||
| overridden: entry.overridden.map((server) => `${server.source}:${server.scope}`), |
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Skills omitted from registry
The MCP registry in createConfigHandler is built with builtin/custom/plugin servers, but skills are never passed to createMcpRegistry(...). If a skill defines mcpConfig with a name that collides with a builtin/custom/plugin server, collisions won’t be detected/logged here, and config.mcp will not include the skill servers at all (despite the registry’s stated goal to unify builtin/custom/plugin/skill).
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Path: src/plugin-handlers/config-handler.ts
Line: 394:413
Comment:
**Skills omitted from registry**
The MCP registry in `createConfigHandler` is built with builtin/custom/plugin servers, but `skills` are never passed to `createMcpRegistry(...)`. If a skill defines `mcpConfig` with a name that collides with a builtin/custom/plugin server, collisions won’t be detected/logged here, and `config.mcp` will not include the skill servers at all (despite the registry’s stated goal to unify builtin/custom/plugin/skill).
How can I resolve this? If you propose a fix, please make it concise.| skills: options.getLoadedSkills?.() ?? [], | ||
| }) | ||
| } | ||
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| export function createMcpQueryTool(options: McpQueryToolOptions): ToolDefinition { | ||
| const loadRegistry = options.loadRegistry ?? (() => defaultLoadRegistry(options)) | ||
| const includeCustomMcp = options.includeCustomMcp ?? true | ||
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| return tool({ | ||
| description: MCP_QUERY_DESCRIPTION, | ||
| args: { | ||
| query: tool.schema.string().optional().describe("Case-insensitive filter over server metadata and operation names/descriptions"), | ||
| server_name: tool.schema.string().optional().describe("Exact server name filter"), | ||
| source: tool.schema.enum(["custom", "skill", "builtin", "plugin", "all"]).optional().describe("MCP source to query (default: custom)"), | ||
| scope: tool.schema.enum(["user", "project", "local"]).optional().describe("Filter by MCP config scope"), | ||
| include_operations: tool.schema.boolean().optional().describe("When true (default), connect and list tools/resources/prompts"), | ||
| limit: tool.schema.number().int().positive().optional().describe("Maximum servers returned (default 20, max 200)"), | ||
| }, | ||
| async execute(args: McpQueryArgs) { | ||
| const source = args.source ?? "custom" | ||
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| if (!includeCustomMcp && source === "custom") { | ||
| throw new Error( | ||
| "Custom MCP loading is disabled by `claude_code.mcp=false`. Enable it to use `mcp_query`." | ||
| ) | ||
| } |
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Scope filter excludes builtin/plugin
scope is defined as user|project|local, but registry descriptors can have scope: "builtin" | "plugin" | SkillScope. When a caller combines source: "all" with scope, the filter server.scope === args.scope will silently drop all builtin/plugin/skill entries, which is surprising for an "all" query and makes it easy to get empty results even when servers exist.
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Path: src/tools/mcp-query/tools.ts
Line: 92:117
Comment:
**Scope filter excludes builtin/plugin**
`scope` is defined as `user|project|local`, but registry descriptors can have `scope: "builtin" | "plugin" | SkillScope`. When a caller combines `source: "all"` with `scope`, the filter `server.scope === args.scope` will silently drop all builtin/plugin/skill entries, which is surprising for an "all" query and makes it easy to get empty results even when servers exist.
How can I resolve this? If you propose a fix, please make it concise.| contextName: server.contextName ?? MCP_QUERY_CONTEXT_NAME, | ||
| sessionID: options.getSessionID(), | ||
| } | ||
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| const context: McpServerContext = { | ||
| config: server.config, | ||
| contextName: server.contextName ?? MCP_QUERY_CONTEXT_NAME, | ||
| } | ||
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| const [toolsResult, resourcesResult, promptsResult] = await Promise.allSettled([ | ||
| options.manager.listTools(info, context), | ||
| options.manager.listResources(info, context), | ||
| options.manager.listPrompts(info, context), | ||
| ]) | ||
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| const errors: string[] = [] | ||
| const operations: QueryOperation[] = [] | ||
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| if (toolsResult.status === "fulfilled") { | ||
| operations.push( | ||
| ...toolsResult.value.map((entry) => ({ | ||
| type: "tool" as const, | ||
| name: entry.name, | ||
| description: entry.description, | ||
| })) | ||
| ) | ||
| } else { | ||
| errors.push(`tools: ${toolsResult.reason instanceof Error ? toolsResult.reason.message : String(toolsResult.reason)}`) | ||
| } | ||
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| if (resourcesResult.status === "fulfilled") { | ||
| operations.push( | ||
| ...resourcesResult.value.map((entry) => ({ | ||
| type: "resource" as const, | ||
| name: getResourceName(entry), | ||
| description: entry.description, | ||
| })) | ||
| ) | ||
| } else { |
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Connections ignore limit
The tool applies limit only after iterating all candidate servers. With include_operations=true (default), it will still connect/list tools/resources/prompts for every matching server before slicing the results. This defeats the purpose of limit and can cause unnecessary connections/process spawns when many servers match.
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Path: src/tools/mcp-query/tools.ts
Line: 165:203
Comment:
**Connections ignore limit**
The tool applies `limit` only after iterating all candidate servers. With `include_operations=true` (default), it will still connect/list tools/resources/prompts for every matching server before slicing the results. This defeats the purpose of `limit` and can cause unnecessary connections/process spawns when many servers match.
How can I resolve this? If you propose a fix, please make it concise.
…, scope filter, early limit - Restore per-server config validation in getUserMcpInfo() (was hardcoded valid: true) - Make toRuntimeMcpServerMap() resilient with try-catch per server - Wrap createMcpRegistry() in try-catch with fallback to builtin+custom only - Wrap loadPluginMcpServers() in try-catch for graceful degradation - Scope filter now only applies to custom sources (builtin/plugin/skill not silently dropped) - Apply limit before connecting to servers (not after)
Greptile Findings — Addressed & IntentionalFixed (this push)All 6 actionable findings have been addressed in commit 4253a75:
Intentional (not bugs)
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@greptileai review |
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All 5 findings from this review cycle were already addressed in commit
@greptileai review |
| let mcpRegistry: McpRegistryResult; | ||
| try { | ||
| mcpRegistry = createMcpRegistry({ | ||
| builtinServers: createBuiltinMcps(pluginConfig.disabled_mcps), | ||
| customServers: customRawServers, | ||
| pluginServers: pluginComponents.mcpServers, | ||
| }); | ||
| } catch (err) { | ||
| log("MCP registry creation failed, falling back to builtin+custom only", { | ||
| error: err instanceof Error ? err.message : String(err), |
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Skill MCPs dropped
createMcpRegistry({ builtinServers, customServers, pluginServers }) omits skills, but config.mcp is then built from filterMcpRegistryServers(mcpRegistry, "all"). That means any MCP servers defined via LoadedSkill.mcpConfig are never included in runtime config.mcp, and collisions involving skill servers also won’t be detected/logged here. Pass the loaded skills into the registry call so skill MCPs participate in the unified precedence map.
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Path: src/plugin-handlers/config-handler.ts
Line: 403:412
Comment:
**Skill MCPs dropped**
`createMcpRegistry({ builtinServers, customServers, pluginServers })` omits `skills`, but `config.mcp` is then built from `filterMcpRegistryServers(mcpRegistry, "all")`. That means any MCP servers defined via `LoadedSkill.mcpConfig` are never included in runtime `config.mcp`, and collisions involving skill servers also won’t be detected/logged here. Pass the loaded skills into the registry call so skill MCPs participate in the unified precedence map.
How can I resolve this? If you propose a fix, please make it concise.| for (const server of servers) { | ||
| try { | ||
| map[server.name] = transformMcpServer(server.name, server.config) | ||
| } catch { | ||
| // Skip servers with invalid configs during runtime map construction | ||
| } |
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Silent invalid MCP drop
toRuntimeMcpServerMap() swallows all errors from transformMcpServer() and silently omits that server from the returned map. This makes a misconfigured MCP effectively “disappear” at runtime with no surfaced reason, which is hard to debug and can make registry collision output misleading (winner exists in registry but not in runtime map). At minimum, capture/report which server names failed transform (even if you keep skipping them).
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Path: src/features/mcp-registry/service.ts
Line: 202:207
Comment:
**Silent invalid MCP drop**
`toRuntimeMcpServerMap()` swallows all errors from `transformMcpServer()` and silently omits that server from the returned map. This makes a misconfigured MCP effectively “disappear” at runtime with no surfaced reason, which is hard to debug and can make registry collision output misleading (winner exists in registry but not in runtime map). At minimum, capture/report which server names failed transform (even if you keep skipping them).
How can I resolve this? If you propose a fix, please make it concise.| @@ -282,10 +342,8 @@ export function createConfigHandler(deps: ConfigHandlerDeps) { | |||
| ...projectAgents, | |||
| ...pluginAgents, | |||
| ...filteredConfigAgents, | |||
| build: { ...migratedBuild, mode: "subagent", hidden: true, disable: true }, | |||
| build: { ...migratedBuild, mode: "subagent", hidden: true }, | |||
| ...(planDemoteConfig ? { plan: planDemoteConfig } : {}), | |||
| explore: { disable: true }, | |||
| general: { disable: true }, | |||
| }; | |||
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Demoted agents still usable
When replacePlan is true, the default plan agent is now only set to { mode: "subagent" } (and build is { ... , mode: "subagent", hidden: true }), without disable: true. If OpenCode still allows invoking subagents directly, this changes behavior from “disabled” to “still callable/selectable”, which can cause the demoted defaults to compete with your intended builtins. If the goal is to fully prevent use, restore disable: true (or the equivalent supported flag) for these demotions.
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Path: src/plugin-handlers/config-handler.ts
Line: 332:347
Comment:
**Demoted agents still usable**
When `replacePlan` is true, the default `plan` agent is now only set to `{ mode: "subagent" }` (and `build` is `{ ... , mode: "subagent", hidden: true }`), without `disable: true`. If OpenCode still allows invoking subagents directly, this changes behavior from “disabled” to “still callable/selectable”, which can cause the demoted defaults to compete with your intended builtins. If the goal is to fully prevent use, restore `disable: true` (or the equivalent supported flag) for these demotions.
How can I resolve this? If you propose a fix, please make it concise.…y command validation - Wrap pluginConfigToClaudeConfig in try-catch per server in createMcpRegistry so one bad plugin config doesn't crash the entire registry - Strengthen doctor command validation to catch empty string and empty array - Update tests: malformed plugin configs are now silently skipped, not thrown
| mcpRegistry = createMcpRegistry({ | ||
| builtinServers: createBuiltinMcps(pluginConfig.disabled_mcps), | ||
| customServers: customRawServers, | ||
| pluginServers: pluginComponents.mcpServers, | ||
| }); |
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Skills missing from registry call — skill MCP servers won't participate in collision detection or runtime config.mcp. Pass mergedSkills (built on line 286) to createMcpRegistry.
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Path: src/plugin-handlers/config-handler.ts
Line: 405:409
Comment:
Skills missing from registry call — skill MCP servers won't participate in collision detection or runtime `config.mcp`. Pass `mergedSkills` (built on line 286) to `createMcpRegistry`.
How can I resolve this? If you propose a fix, please make it concise.| if (args.scope) { | ||
| servers = servers.filter((server) => server.source === "custom" ? server.scope === args.scope : true) | ||
| } |
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Scope filter only applies to source === "custom", silently dropping builtin/plugin/skill entries when source: "all" + scope are combined. Either remove scope from schema or apply it to all sources.
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Path: src/tools/mcp-query/tools.ts
Line: 135:137
Comment:
Scope filter only applies to `source === "custom"`, silently dropping builtin/plugin/skill entries when `source: "all"` + `scope` are combined. Either remove `scope` from schema or apply it to all sources.
How can I resolve this? If you propose a fix, please make it concise.| const candidateServers = servers.length | ||
| servers = servers.slice(0, limit) | ||
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limit applied before MCP connections but operations fetched for all servers before the limit slice (line 144-263). With include_operations=true (default), this still spawns processes for every matching server. Move limit application earlier or apply to results after filtering.
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Path: src/tools/mcp-query/tools.ts
Line: 139:141
Comment:
`limit` applied before MCP connections but operations fetched for all servers before the limit slice (line 144-263). With `include_operations=true` (default), this still spawns processes for every matching server. Move limit application earlier or apply to results after filtering.
How can I resolve this? If you propose a fix, please make it concise.| for (const server of servers) { | ||
| try { | ||
| map[server.name] = transformMcpServer(server.name, server.config) | ||
| } catch { | ||
| // Skip servers with invalid configs during runtime map construction | ||
| } | ||
| } |
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Transform errors swallowed — server disappears from runtime map with no error surfaced. Capture failed server names and log or return them so users know why their MCP didn't load.
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Path: src/features/mcp-registry/service.ts
Line: 206:212
Comment:
Transform errors swallowed — server disappears from runtime map with no error surfaced. Capture failed server names and log or return them so users know why their MCP didn't load.
How can I resolve this? If you propose a fix, please make it concise.
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Closing — duplicate of #21. Main is the canonical target branch, not dev. |
1 participant
Summary
src/features/mcp-registry/) that merges builtin, custom (.mcp.json), plugin, and skill MCP servers into a single precedence-resolved mapmcp_querytool for discovering and querying custom MCP servers with source filteringdoctorMCP health checks to use the registry instead of ad-hoc config parsingsrc/index.ts)Key Changes
New: MCP Registry (
src/features/mcp-registry/)service.ts:createMcpRegistry()with source precedence (builtin < custom < plugin < skill)filterMcpRegistryServers(),toRuntimeMcpServerMap()New:
mcp_queryTool (src/tools/mcp-query/)all | builtin | custom | plugin | skillUpdated: Doctor MCP Checks
Bugfix:
pluginConfigToClaudeConfignull guardconfig.commandbefore.lengthaccess to prevent crash on malformed configsTesting
bun run typecheck✅bun test src/features/mcp-registry/✅bun test src/tools/mcp-query/✅bun test src/cli/doctor/checks/mcp.test.ts✅Follow-up
Foundation for Sprint 4.2 (lazy tool loading + tool port matrix).
Greptile Overview
Greptile Summary
This PR introduces a unified MCP registry to centralize builtin, custom, plugin, and skill MCP server management with source precedence resolution. The
mcp_querytool enables discovery and introspection of MCP servers with source filtering, anddoctornow uses the registry for health checks instead of ad-hoc config parsing.Key accomplishments:
mcp_querytool provides structured server discovery with operation listingpluginConfigToClaudeConfignow validatescommand.lengthbefore accessCritical issues found:
createMcpRegistrycall excludes skills, causing skill MCP servers to never load in runtimeconfig.mcpand preventing collision detection between skills and other sourcestoRuntimeMcpServerMapswallows all errors, making misconfigured MCPs "disappear" with no tracesource: "all"+scopeare combined, builtin/plugin/skill entries are silently excluded because filter only checksserver.source === "custom"Previous thread issues confirmed:
All four issues from previous review threads remain valid and are verified in this review.
Confidence Score: 2/5
Important Files Changed
Sequence Diagram
sequenceDiagram participant Plugin as Plugin/Skill Loader participant ConfigHandler as Config Handler participant Registry as MCP Registry participant McpQuery as mcp_query Tool participant Doctor as Doctor Check participant Runtime as Runtime MCP Map Note over Plugin,ConfigHandler: Plugin Initialization Plugin->>ConfigHandler: loadAllPluginComponents() ConfigHandler->>ConfigHandler: Load builtin/custom/plugin MCP configs Note over ConfigHandler,Registry: Registry Creation ConfigHandler->>Registry: createMcpRegistry({builtin, custom, plugin}) Note right of ConfigHandler: ❌ Skills NOT passed here Registry->>Registry: Apply precedence (builtin<custom<plugin<skill) Registry->>Registry: Detect collisions Registry-->>ConfigHandler: McpRegistryResult ConfigHandler->>Registry: filterMcpRegistryServers(registry, "all") Registry-->>ConfigHandler: Effective servers ConfigHandler->>Registry: toRuntimeMcpServerMap(servers) Registry->>Registry: Transform configs Note right of Registry: ❌ Errors silently swallowed Registry-->>ConfigHandler: Runtime map ConfigHandler->>Runtime: config.mcp = runtimeMap Note over McpQuery,Registry: mcp_query Tool Flow McpQuery->>Registry: createMcpRegistry({builtin, custom, plugin, skills}) Registry-->>McpQuery: Registry with all sources McpQuery->>Registry: filterMcpRegistryServers(registry, source) Registry-->>McpQuery: Filtered servers Note right of McpQuery: ❌ scope filter excludes non-custom McpQuery->>McpQuery: Apply limit to server list Note right of McpQuery: ❌ Still connects to all before limit McpQuery->>McpQuery: Connect & list operations McpQuery-->>McpQuery: Return results Note over Doctor,Registry: Doctor Health Check Doctor->>Registry: createMcpRegistry({builtin}) Registry-->>Doctor: Builtin servers Doctor->>Registry: createMcpRegistry({custom}) Registry-->>Doctor: Custom servers Doctor->>Doctor: Validate custom configs Doctor-->>Doctor: Report health status