refactor(ai): Rename mcp-stdio.mjs to mcp-server.mjs (#9534)

Author: tobiu

…mcp/server/github-workflow/mcp-stdio.mjs …cp/server/github-workflow/mcp-server.mjsai/mcp/server/github-workflow/mcp-stdio.mjs renamed to ai/mcp/server/github-workflow/mcp-server.mjs ai/mcp/server/github-workflow/mcp-stdio.mjs renamed to ai/mcp/server/github-workflow/mcp-server.mjs

@@ -412,7 +412,7 @@ class HealthService extends Base {
 
     /**
      * Records the result of startup summarization attempt.
-     * Called by the startup sequence in mcp-stdio.mjs
+     * Called by the startup sequence in mcp-server.mjs
      * @param {string} status  One of: 'completed', 'failed', 'skipped'
      * @param {Object} details Additional information about the summarization
      */

…/mcp/server/knowledge-base/mcp-stdio.mjs …mcp/server/knowledge-base/mcp-server.mjsai/mcp/server/knowledge-base/mcp-stdio.mjs renamed to ai/mcp/server/knowledge-base/mcp-server.mjs ai/mcp/server/knowledge-base/mcp-stdio.mjs renamed to ai/mcp/server/knowledge-base/mcp-server.mjs

@@ -1599,7 +1599,7 @@ The beauty of this pattern is that **services can depend on each other** without
 1. **`ChromaManager`** initializes and establishes the ChromaDB connection
 2. **`DatabaseLifecycleService`** waits for `ChromaManager.ready()` and starts ChromaDB
 3. **`SessionService`** waits for `DatabaseLifecycleService.ready()` and performs summarization
-4. **`mcp-stdio.mjs`** waits for `SessionService.ready()` and starts the MCP server
+4. **`mcp-server.mjs`** waits for `SessionService.ready()` and starts the MCP server
 
 All of this happens **automatically and in the correct order**, with zero race conditions. From the main entry point:
 

ai/mcp/server/memory-core/mcp-stdio.mjs ai/mcp/server/memory-core/mcp-server.mjsai/mcp/server/memory-core/mcp-stdio.mjs renamed to ai/mcp/server/memory-core/mcp-server.mjs

@@ -17,7 +17,7 @@ $origPATH = $env:PATH
 $env:PATH = ($env:PATH -split ';' | Where-Object { $_ -notmatch 'GitHub CLI' -and $_ -notmatch 'GitHub' }) -join ';'
 
 # Start the MCP stdio server in this session (gh will be hidden)
-node C:/dev/open_source/neo/ai/mcp/server/github-workflow/mcp-stdio.mjs --debug
+node C:/dev/open_source/neo/ai/mcp/server/github-workflow/mcp-server.mjs --debug
 
 # When finished, restore your PATH
 $env:PATH = $origPATH
@@ -31,7 +31,7 @@ $env:PATH = $origPATH
 Alternative single-command test (no session PATH change)
 
 ```powershell
-cmd /C "set PATH=C:\Windows\System32;C:\Windows; & node C:\dev\open_source\neo\ai\mcp\server\github-workflow\mcp-stdio.mjs --debug"
+cmd /C "set PATH=C:\Windows\System32;C:\Windows; & node C:\dev\open_source\neo\ai\mcp\server\github-workflow\mcp-server.mjs --debug"
 ```
 
 Runbook / Remediation

ai/mcp/server/memory-core/services/HealthService.mjs

@@ -67,7 +67,7 @@ It is important to understand that **MCP is just a transport layer**.
 
 In the Neo.mjs Agent OS, the actual business logic (searching vectors, syncing GitHub, saving memories) lives inside **Services** (e.g., `QueryService`, `IssueService`). These are **Neo.mjs Singleton Classes** that exist independently of any server.
 
-*   **The MCP Server** (`mcp-stdio.mjs`) is just a thin wrapper. It exposes these services to the outside world via the Model Context Protocol.
+*   **The MCP Server** (`mcp-server.mjs`) is just a thin wrapper. It exposes these services to the outside world via the Model Context Protocol.
 *   **The AI SDK** (`ai/services.mjs`) imports these **Services** directly.
 
 ### The `initAsync` Pattern

ai/mcp/server/neural-link/mcp-stdio.mjs ai/mcp/server/neural-link/mcp-server.mjsai/mcp/server/neural-link/mcp-stdio.mjs renamed to ai/mcp/server/neural-link/mcp-server.mjs

@@ -120,7 +120,7 @@ The server is highly configurable via `config.mjs` or a custom configuration fil
 ### Usage
 
 ```bash readonly
-node ai/mcp/server/github-workflow/mcp-stdio.mjs -c ./my-config.json
+node ai/mcp/server/github-workflow/mcp-server.mjs -c ./my-config.json
 ```
 
 ### Configuration File Format

learn/blog/context-engineering-done-right.md

@@ -99,7 +99,7 @@ The server supports loading a custom configuration file via the `-c` or `--confi
 ### Usage
 
 ```bash readonly
-node ai/mcp/server/memory-core/mcp-stdio.mjs -c ./my-config.json
+node ai/mcp/server/memory-core/mcp-server.mjs -c ./my-config.json
 ```
 
 ### Configuration File Format