feat(mcp): add project management tools

[juliusmarminge]

Problem

Agents can work inside projects but cannot discover, register, clone, configure, or safely remove project records through T3's MCP boundary. Existing project mutations also drop defaultThreadEnvMode and faviconPath along some client/server paths.

Change

• Add typed t3_project_list, t3_project_read, t3_project_create, t3_project_update, and t3_project_delete tools backed by ProjectService.
• Support existing directories, explicit missing-directory creation, and mutually exclusive URL or provider/repository clone sources through the existing clone service.
• Preserve omitted versus explicit-null project settings end to end, including client-runtime commands, events, projections, and websocket mutations.
• Bound project listing before per-project configuration reads and keep full scripts on t3_project_read.
• Recover only a completed clone whose canonical repository root and remote match the requested source, while serializing overlapping clone/create attempts.
• Guard nonempty deletion across active, archived, and app-owned child threads; explicit cascade uses normal thread-delete commands.

Behavior

Project reads expose roots, titles, model defaults, scripts, icons, and project/file/global/effective workspace modes. Clone creation never publishes or adopts unrelated existing contents. Project removal never deletes repository, worktree, or workspace files. Delete counts are per attempt; a retry after deletion returns alreadyDeleted: true and a zero count.

Validation

• Focused project MCP, clone-retry/overlap, project service, contract, client command, registration, and project env-mode tests.
• @t3tools/contracts, @t3tools/client-runtime, and server targeted typechecks.
• Targeted lint for changed project MCP, contract, and client-runtime files.

Dependency

Targets the immutable rollout base agents/mcp-controls/base-490318a at 490318afa505d3d033295eca12d7e62b4b922725. This is the bottom layer of native stack #8710; #8678 is the dependent upper layer.

Implemented by GPT-5.6-Sol via Codex in T3 Code.

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[macroscopeapp]

Effect service conventions: one violation found in apps/server/src/mcp/ProjectMcpService.ts (standalone service shape interface). The rest of the new MCP service module, toolkit, handlers, and contracts follow the repository's Effect conventions.

^{Posted via Macroscope — Effect Service Conventions}

[github-actions]

Thread transfer impact

⚠️ The latest CI run did not produce a thread transfer result for 945b99f.

This comment will update automatically after the next completed run.

[cursor]

Cursor Bugbot has reviewed your changes using high effort and found 1 potential issue.

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[macroscopeapp]

Approvability

Verdict: Not approved

Macroscope's review found this PR not approvable — This PR adds production MCP tools that can create, clone, update, and delete projects and cascade-delete their thread records, with changes across shared orchestration and source-control paths. It also changes persisted project defaults and effective workspace-mode behavior, making the scope and impact unsuitable for automatic approval.

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[macroscopeapp]

Effect service conventions: one minor import-hygiene issue in the new test module. The service definition itself (inline Context.Service interface, ProjectMcpService["Service"][...] annotations, namespaced module imports, make + layer order) follows the sibling WorktreeMcpService.ts conventions.

^{Posted via Macroscope — Effect Service Conventions}

[macroscopeapp]

One convention issue found: an aliased layer import in apps/server/src/mcp/ProjectMcpService.test.ts erases the service module namespace (and is shadowed later in the file). The service definition itself (inline Context.Service interface, make, typed layer, Foo["Service"] annotations, dependencies acquired from the environment) follows the conventions.

^{Posted via Macroscope — Effect Service Conventions}