MCP server: renaming/aliasing a tool silently drops it from stored agent definitions
## Summary
When an MCP tool is renamed (or consolidated) and the old name is preserved as an alias for backward compatibility, **stored agent definitions that reference the old tool name silently lose that tool**. The agent keeps running without the capability, and no error or warning is surfaced.
This is reproducible today. Two aliases already ship:
- `gitlab_search` → `search` (`app/services/mcp/tools/search/search_service.rb:25`)
- `gitlab_merge_request_search` → `list_merge_requests` (`app/services/mcp/tools/merge_requests/list_merge_requests_service.rb:83`)
Any agent definition saved before those renames has been missing that tool ever since.
## Root cause
### 1. Stored alias names are dropped
`Ai::DuoWorkflows::McpConfigService#mcp_tools_for_agent` builds an agent's tool set by intersecting the agent's stored tool names against the set of currently-available tools:
```ruby
available = all_mcp_tools # = Mcp::Tools::Manager.new.list_tools.keys
((built_in_names + Array(agent_mcp_tools)) & available).uniq
```
`list_tools` returns **canonical names only**. Aliases live in a separate `alias_map` (`Manager#build_alias_map`) that is consulted only on the `tools/call` path via `resolve_alias`. So an alias resolves correctly when a tool is *called*, but a stored `mcp_tools: ["old_name"]` entry is dropped by `& available`.
### 2. API-backed tools cannot declare aliases
`Mcp::Tools::Base::ApiTool` is a **single class instantiated once per route** (`Manager#discover_api_tools`). A class-level `self.tool_aliases` would therefore be shared by every API tool, so it is structurally unusable for them — aliases must be per-instance, read from `route_setting :mcp`.
Note this is *not* simply a matter of `ApiTool` not inheriting `Base::BaseService`; making it inherit would not fix the per-route problem.
`doc/development/duo_agent_platform/mcp/_index.md:519` currently claims "Aliases work for all tool types: custom, GraphQL, API, and aggregated tools", which is false for API tools.
## Current behavior
Renaming or aliasing a tool causes stored agent definitions naming the old tool to silently lose it, with no error. API-backed tools cannot declare an alias at all.
## Expected behavior
A tool preserved via an alias remains resolvable for stored agent definitions, and API-backed tools can declare aliases.
## Proposed fix
Resolve aliases to canonical names on the way **into** the intersection. Do **not** add aliases to `list_tools`.
`list_tools` must stay canonical because it is shared by consumers that would break:
- the MCP `tools/list` response — aliases would appear to every client as duplicate, fully-schema'd tools and inflate the tool budget, defeating the point of consolidation
- `Ai::Catalog::McpTool.fixed_items` — aliases would become newly *selectable* in the agent builder, the opposite of deprecating a name
- `_index.md:518` documents `list_tools` as canonical-only, and `manager_spec.rb` guards it
Canonical output is required rather than merely preferred: `gitlab_enabled_tools` becomes the `x-gitlab-enabled-mcp-server-tools` header, which returns to the MCP server as `allowed_tools`, and `ListTools#invoke` filters that against canonical keys while logging unknown names. Emitting an alias would drop the tool one layer later and log a warning.
### MR A — stop dropping alias-named tools
- `McpConfigService#mcp_tools_for_agent`: map stored `agent_mcp_tools` through `Manager#resolve_alias` before `& all_mcp_tools`
- Make `Manager#resolve_alias` public
- Do **not** resolve `built_in_names`. Built-in tool names are a separate namespace, and an MCP alias colliding with a built-in name would silently rewrite the built-in
Verifiable against the two aliases that already exist, so it carries no dependency on MR B.
### MR B — let API tools declare aliases
- `Base::ApiTool#tool_aliases`, sourced from `settings[:tool_aliases]`
- `BaseService#tool_aliases` instance-level delegator to the existing class method
- `Manager#build_alias_map`: use the instance method rather than `tool.class`
- Correct `_index.md:519`, and note that `tool_aliases:` on a route carrying `aggregators:` is dead config
Declaring an actual production alias belongs in the consolidation MR, not here. Once a `readOnlyHint` route gains an alias, the pre-approved tool list grows and the hardcoded expectations in `workflows_spec.rb` and `mcp_config_service_spec.rb` will fail by design — those lists are deliberate change-detectors.
## Out of scope
- **`notifications/tools/list_changed`** — tracked separately in #582750
- **Alias-with-default-args** (old name → new tool plus a forced argument) — a different mechanism; it changes `tools/call` argument handling rather than name resolution, and needs a decision on merge/override semantics against caller-supplied arguments. Should be its own issue, blocked on the consolidation design
- **`ListTools#invoke` does not alias-resolve `allowed_tools`** — same bug class one layer up. During a rolling deploy, a session whose header was built by a pre-rename node has the tool filtered out by a post-rename node. Worth a linked follow-up
## Why it matters
This blocks backward-compatible tool consolidation. The `get_merge_request` consolidation needs stored agent definitions referencing old names (for example `get_merge_request_commits`) to keep working.
## References
- Discussion: https://gitlab.com/groups/gitlab-org/-/work_items/20222#note_3557221499
- Parent epic: https://gitlab.com/groups/gitlab-org/-/epics/22414
issue
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