### What problem does this PR solve?
When multiple MCP servers expose tools with the same name, the agent
currently registers those tools using their original MCP names. This can
lead to two issues:
- later MCP tools may overwrite earlier ones in the agent tool map
- duplicate function names may be exposed to the LLM
This PR fixes duplicate MCP tool-name handling by applying the same
indexed naming strategy already used for native agent tools. Native
tools are exposed with generated names such as `<tool_name>_<index>` to
avoid collisions, and MCP tools now follow the same convention for
consistency.
Specifically, this PR:
- assigns unique indexed function names to MCP tools exposed to the LLM
- preserves each MCP tool's original server-side name in an
`MCPToolBinding`
- dispatches MCP calls using the original MCP tool name while keeping
the indexed name in the agent tool map
- allows MCP metadata conversion to override only the OpenAI function
name without modifying the original MCP tool metadata
### Type of change
- [x] Bug Fix (non-breaking change which fixes an issue)
### Validation
The validation was performed using two MCP servers. Both servers exposed
a tool with the same name: `mcp0`. Both tools take no input parameters.
**MCP Server One:**
<img width="1780" height="625" alt="ONE"
src="https://github.com/user-attachments/assets/801a2654-fc10-4b71-b31c-81841fd40c55"
/>
**MCP Server Two:**
<img width="1777" height="624" alt="Second"
src="https://github.com/user-attachments/assets/c095151d-7bdf-47c8-9bfe-6aaf4a01b944"
/>
**Before the fix:**
When invoking `mcp0`, only the `mcp0` tool from the MCP server injected
later could be called successfully. As shown below, both `mcp0` tools
were present, but only the later-registered one was actually invokable.
<img width="694" height="935" alt="Three"
src="https://github.com/user-attachments/assets/3b9d7ab2-1765-492c-b8e0-bf05a69933ca"
/>
**After the fix:**
Both `mcp0` tools can now be invoked correctly.
<img width="737" height="1095" alt="F"
src="https://github.com/user-attachments/assets/6e896627-2b7f-41bb-becc-daa0c73ff58f"
/>
<img width="730" height="1090" alt="six"
src="https://github.com/user-attachments/assets/aba75593-26ae-4e3b-951d-b45ff177fd32"
/>
### What problem does this PR solve?
Resolves#12105
This PR fixes two MCP tool call issues in
`common/mcp_tool_call_conn.py`.
First, the timeout passed to `tool_call(..., timeout=...)` was only
applied to the outer `future.result(...)` wait, but was not forwarded to
the internal MCP request. As a result, callers could pass a longer
timeout while the actual MCP request still failed after the default
internal timeout.
Second, the MCP tool call result handling assumed `result.content[0]`
always existed. If an MCP server returned an empty content list, this
could raise an exception unexpectedly.
This PR fixes both issues by:
- forwarding the external `timeout` value to the internal MCP request
timeout
- returning a clear message when the MCP server returns empty content
instead of indexing into an empty list
### Type of change
- [x] Bug Fix (non-breaking change which fixes an issue)
- [ ] New Feature (non-breaking change which adds functionality)
- [ ] Documentation Update
- [ ] Refactoring
- [ ] Performance Improvement
- [ ] Other (please describe)
### What problem does this PR solve?
As title.
### Type of change
- [x] New Feature (non-breaking change which adds functionality)
Co-authored-by: Liu An <asiro@qq.com>
