feat: custom MCP server configuration per session and project

[ambient-code]

Summary

• Add mcpServers field to AgenticSession and ProjectSettings CRDs for custom server config (custom servers map + disabled list)
• Backend accepts mcpServers in create/update session requests, allows MCP-only updates on running sessions (persisted for next restart)
• New backend endpoints GET/PUT /projects/:name/mcp-servers for project-level MCP defaults
• Operator passes session and project MCP config to runner pods via CUSTOM_MCP_SERVERS and PROJECT_MCP_SERVERS env vars
• Runner merges MCP configs in priority order: defaults < project < session, then removes disabled servers
• Session settings modal expanded to max-w-5xl with MCP management UI: add custom servers, disable/enable defaults, remove custom servers
• New project settings MCP section for project-wide MCP server defaults
• 9 unit tests for runner config merging logic

Test plan

• Verify CRD schema applies cleanly (kubectl apply -f components/manifests/base/crds/)
• Create a session with custom mcpServers in the request body
• Verify custom MCP servers appear in the running session
• Disable a default server (e.g. context7) and verify it's excluded on next restart
• Add a custom HTTP MCP server via session settings modal
• Configure project-level MCP defaults and verify new sessions inherit them
• Verify session-level config overrides project-level config
• Run runner unit tests: cd components/runners/ambient-runner && python -m pytest tests/test_mcp_config.py -v
• Run frontend tests: cd components/frontend && npx vitest run

Closes #1249

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🤖 Ambient Session

[ambient-code]

This PR implements all 4 requirements from #1249:

1. Enable/disable/add/remove MCP servers from running sessions - Session settings modal now has full MCP management (add custom HTTP/SSE/Stdio servers, disable/enable default servers, remove custom servers). Changes are persisted in the CRD and take effect on session restart.

2. MCP config persisted on session stop/start - MCP configuration is stored in the AgenticSession CRD spec.mcpServers field. The operator passes this config to the runner pod as environment variables, which the runner merges with platform defaults.

3. Project-level MCP configuration - New spec.mcpServers field on ProjectSettings CRD, new backend endpoints (GET/PUT /projects/:name/mcp-servers), and a new "MCP Servers" card in project settings UI. Project defaults are inherited by all sessions.

4. Wider session settings modal - Modal widened from max-w-4xl to max-w-5xl, height increased from 540px/70vh to 600px/80vh, title changed from "Settings" to "Session Settings".

🤖 Session

[Gkrumbach07]

@ambient-code can you verify all edge cases are handled, that this works end to end. i want a comment with your findings walking me through how this feature works

[ambient-code]

End-to-End Review: Custom MCP Server Configuration (#1249)

I reviewed every layer of this feature — CRDs, backend, operator, runner, and frontend. Here's a walkthrough of how it works and what I found.

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How the feature works end-to-end

1. CRD Schema (data model)
Both AgenticSession and ProjectSettings CRDs gain an optional mcpServers field with two sub-fields:

• custom: a map of server name → arbitrary config object (x-kubernetes-preserve-unknown-fields: true allows stdio/http/sse configs)
• disabled: a string array of default server names to turn off

Fully backward-compatible — existing CRs without mcpServers are unaffected.

2. Backend API (CRUD)

• Create session: mcpServers is accepted in CreateAgenticSessionRequest and stored in the CR spec.
• Update session: A new isMCPOnlyUpdate guard allows MCP config changes on running sessions (other spec fields are still blocked with 409). The config is persisted for the next restart.
• Project-level: New GET/PUT /api/projects/:name/mcp-servers endpoints read/write mcpServers on the ProjectSettings CR.
• Auth is correct throughout — all handlers use GetK8sClientsForRequest(c) so RBAC is delegated to K8s.

3. Operator (env var injection)
When the operator creates a runner pod, it:

• Reads spec.mcpServers from the session CR → serializes as JSON → sets CUSTOM_MCP_SERVERS env var
• Reads spec.mcpServers from the project's ProjectSettings CR → serializes as JSON → sets PROJECT_MCP_SERVERS env var
• If either CR/field is absent, the corresponding env var is simply not set (graceful no-op)

4. Runner (merge logic)
load_mcp_config() merges three layers with clear priority:

Platform defaults (.mcp.json) < Project-level (PROJECT_MCP_SERVERS) < Session-level (CUSTOM_MCP_SERVERS)

• dict.update() ensures higher-priority layers overwrite lower ones
• disabled lists from both project and session are combined
• Disabled servers are removed from the final config
• If all servers end up disabled/empty, returns None

5. Frontend UI

• Session Settings Modal: Widened to max-w-5xl / 600px height. New MCP Servers tab shows live server status, custom servers with add/remove, and disable toggles for non-core servers. Core servers (session, corrections, acp, rubric) cannot be disabled.
• Project Settings: New ProjectMcpSection card for managing project-level custom servers and disabled defaults.
• Both use React Query mutations with toast notifications on success/error.

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Edge cases verified

Scenario	Status	Notes
Session has no mcpServers (existing CRs)	✅ Handled	Optional field, all layers gracefully skip
ProjectSettings CR doesn't exist	✅ Handled	Operator silently skips, no env var set
Invalid JSON in env vars	✅ Handled	Runner logs error and skips, other layers still merge
Session and project define same server name	✅ Handled	Session wins via dict.update() order
Disabled list references nonexistent server	✅ Handled	if name in mcp_servers guard prevents KeyError
All servers disabled	✅ Handled	Returns None, runner uses no MCP config
Duplicate server name in UI	✅ Handled	Both session and project UIs check for existing names
Empty name/url/command in UI	✅ Handled	Submit buttons disabled, early returns in handlers
Disabling core platform servers	✅ Handled	UI hides disable button for session/corrections/acp/rubric
Mutation failure in UI	✅ Handled	Toast error shown, dialog stays open for retry, no optimistic updates to roll back
.mcp.json doesn't exist + custom servers	✅ Handled	Starts from empty dict, merges custom servers normally

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Items worth noting (not blockers)

Medium:

1. Session cache invalidation after MCP mutation: useUpdateSessionMcpServers invalidates the MCP status query but not the session detail query. Since McpServersPanel reads session.spec.mcpServers from the parent prop, rapid successive mutations could build on stale state (e.g., add server A, then immediately add server B before refetch → server A lost). Low probability in practice since users don't typically rapid-fire config changes.

2. userEnvVars can override MCP env vars: The operator's replaceOrAppendEnvVars means a user who sets CUSTOM_MCP_SERVERS in environmentVariables would override the operator-computed value. Could be documented as intentional or guarded.

3. No server-side validation of MCP config content: Server names and config objects are stored as-is. No checks for required fields (url for http/sse, command for stdio), name length, or payload size. The CRD's x-kubernetes-preserve-unknown-fields passes everything through. Validation is effectively deferred to the runner.

Low:
4. Project-level disabled list has no core-server protection: The session UI prevents disabling core servers, but the project settings UI accepts any server name in the disabled input (including "session", "corrections", etc.). The runner would remove them.

5. MCP serialization logic is duplicated in three backend locations (create session, update session, update project MCP). Could be extracted to a helper.

6. Corrupt .mcp.json short-circuits the entire merge: Unlike env var parse failures (which are caught and skipped gracefully), a malformed .mcp.json file causes load_mcp_config() to return None entirely, even if custom servers are configured.

7. Missing test for invalid PROJECT_MCP_SERVERS JSON: The runner tests cover invalid CUSTOM_MCP_SERVERS but not the project-level equivalent.

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Test coverage

• Runner: 9 unit tests covering all major merge scenarios (default load, session merge, project merge, session-overrides-project, disable servers, combined disabled, all-disabled, invalid JSON, no-default-file). All passing.
• Frontend: 3 test files updated with useUpdateSessionMcpServers mock. Existing tests pass with the new module structure.
• Backend/Operator: Relies on existing integration test patterns. No new unit tests for the Go handlers, but the code follows established patterns.

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Verdict

The feature is well-structured across all layers with correct merge semantics, proper auth, and good UI/UX. The edge cases that matter for correctness are all handled. The items noted above are improvements to consider in follow-ups, not blockers for merge.

[mergify]

Merge Queue Status

• ✅ Entered queue — 2026-04-08 19:58 UTC · Rule: default
• ✅ Checks passed · on draft merge queue: embarking main (1f254b2) and #1251 together #1254
• ✅ Merged — 2026-04-08 19:59 UTC · at f999e2f2daa12bc62f69e112108f440b6df5429e

This pull request spent 17 seconds in the queue, including 3 seconds running CI.

Required conditions to merge

• #approved-reviews-by >= 1 [🛡 GitHub repository ruleset rule protect-main]
  • feat: custom MCP server configuration per session and project #1251
• #changes-requested-reviews-by = 0 [🛡 GitHub repository ruleset rule protect-main]
  • feat: custom MCP server configuration per session and project #1251