Reorganize Mcp::Tools by domain and drop the redundant Graphql service prefix
## Why
`Mcp::Tools` is currently organized on two competing axes at once, applied inconsistently:
- **Domain** — `work_items/`, `labels/`, `merge_requests/`
- **Implementation kind** — custom / REST (`api_*`) / graphql / aggregated
This leads to inconsistent locations for related tools:
- **Same-domain tools are split by kind.** `get_merge_request_conflicts_service.rb` (custom) sits flat at the top level, while `merge_requests/get_merge_request_notes_*` (graphql) lives in a domain folder. Same domain, two homes.
- **Aggregated tools sit flat at the top level.** `SearchService` and `PipelineService` (`< AggregatedService`) live at the root next to base classes.
- **Base/framework classes are interleaved with concrete tools.** `base_service`, `graphql_service`, `graphql_tool`, `api_tool`, `aggregated_service` sit beside `get_server_version_service` and `get_merge_request_conflicts_service`.
- **The `Graphql` prefix on Service classes carries no signal.** There is no `graphql` folder, the paired Tool classes are unprefixed (`GetWorkItemNotesTool`), and each class already inherits from `GraphqlService`. The new `get_merge_request_notes` tool already ships unprefixed (`GetMergeRequestNotesService`); this converges the rest.
## Guiding principle
- **Folder = domain** (what the tool is about)
- **Base class = kind** (how it's implemented: `CustomService` / `GraphqlService` / `AggregatedService` / `ApiTool`)
- **`manager.rb` registry = dispatch** (`CUSTOM_TOOLS` / `GRAPHQL_TOOLS` / discovered API / aggregated)
Kind is already expressed by the base class **and** the registry bucket — it does not need a third expression as a folder. Domain is the axis currently expressed nowhere consistently; that is the gap to close.
## Proposed structure
```
tools/
. ← get_server_version_service (any non-domain specific service/tool)
base/ ← BaseService, CustomService, GraphqlService, GraphqlTool,
ApiService, ApiTool, AggregatedService, response,
version_helper, icon_config
concerns/
manager.rb ← the one place kind/dispatch lives
merge_requests/ ← get_merge_request_notes_{tool,service}, get_merge_request_conflicts_service
work_items/ ← the 5 existing graphql tools (+ paired services)
labels/ ← search_tool + service
search/ ← search_service (aggregated; domain = search)
pipelines/ ← pipeline_service (aggregated; domain = pipelines)
```
Notes:
- **API tools do not move** — they are discovered from `route_setting :mcp` in `lib/api/**` and wrapped by the generic `ApiTool`. There are no per-tool files for them here.
- **Aggregated tools group by domain** (`search/`, `pipelines/`), not into an `aggregated/` bucket — the aggregated-ness is an implementation strategy, not a domain.
- **Consistent foldering, including domains-of-one** (`search/`). The alternative (singletons flat) is the inconsistency this issue removes.
- Non-domain tools (MCP server only, not related to GitLab data) remain in `tools/` folder
### How to identify a GraphQL tool after the reorg
So the dropped prefix does not hurt discoverability:
1. **File pairing** — GraphQL tools are the only kind with both a `*_tool.rb` (`< GraphqlTool`) and a `*_service.rb` (`< GraphqlService`). A lone `*_service.rb` is custom or aggregated.
2. **Base class** — explicit `< GraphqlService` / `< GraphqlTool` in every file.
3. **`GRAPHQL_TOOLS`** in `manager.rb` is the canonical index.
## Scope
1. Introduce `tools/base/` and move the framework classes into it (update namespaces to match — Zeitwerk requires file path == module path).
2. Move every concrete tool into a domain folder per the tree above.
3. Drop the redundant `Graphql` prefix from the six Service classes (class + file + `manager.rb` registration value + EE overrides + spec files / `describe` blocks). **Keep the agent-facing `tool_name` keys unchanged** (contracts are append-only):
- `Mcp::Tools::WorkItems::GraphqlCreateWorkItemNoteService` → `CreateWorkItemNoteService`
- `Mcp::Tools::WorkItems::GraphqlGetSavedViewWorkItemsService` → `GetSavedViewWorkItemsService`
- `Mcp::Tools::WorkItems::GraphqlGetWorkItemNotesService` → `GetWorkItemNotesService`
- `Mcp::Tools::WorkItems::GraphqlGetWorkItemTypesService` → `GetWorkItemTypesService`
- `Mcp::Tools::WorkItems::GraphqlLinkWorkItemsService` → `LinkWorkItemsService`
- `Mcp::Tools::Labels::GraphqlSearchService` → `Mcp::Tools::Labels::SearchService` (parallels the existing `Labels::SearchTool`; distinct from the aggregated `Search::SearchService`)
4. Update the developer docs to match the new layout and naming:
- `doc/development/duo_agent_platform/mcp/graphql_integration.md` — the hardcoded file paths (`app/services/mcp/tools/graphql_tool.rb`, `graphql_service.rb`) move under `base/`, and the worked example (`GraphqlCreateIssueService` / `app/services/mcp/tools/graphql_create_issue_service.rb`) must drop the prefix and reflect a domain folder.
- `doc/development/duo_agent_platform/mcp/_index.md` — update any `manager.rb` / path references.
## Watch out for
- **Zeitwerk** — every move must update the module nesting to match the new path, or autoloading breaks.
- **EE overrides** under `ee/app/services/ee/mcp/tools/**` (`link_work_items`, aggregated `search`) — they mirror the FOSS paths and must move in lockstep.
- **`manager.rb`** maps (FOSS + EE) reference every class by constant.
- **Specs** referencing these class names, including the schema-locked specs from !240451.
- **`Labels::SearchService` vs `Search::SearchService`** — distinct namespaces, no collision, but name them deliberately.
## Sequencing
Do this **after !240451 merges** (it locks the service schemas in specs and references the current class names).
## Out of scope
- Agent-facing `tool_name` casing (`get_workitem_notes` → `get_work_item_notes`, etc.) — tracked separately.
- Collapsing the `*Tool` / `*Service` two-file pattern into one — a larger framework change; separate spike if desired.
issue
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