Fix mcp/shell stdin hang and robustness

mcp/shell/.gitignore

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+node_modules/
+dist/
+*.log
+.DS_Store

mcp/shell/README.md

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+# MCP Shell Server
+
+A Model Context Protocol (MCP) server that enables executing shell commands via
+`bash`. Designed to be robust, secure, and easy to use for agents.
+
+## Features
+
+- **Execute Shell Commands**: Runs commands via `bash -c`.
+- **Arguments**: Pass arguments safely to the script (accessible as `$1`, `$2`,
+  etc.).
+- **Environment Variables**: Set custom environment variables.
+- **Input (stdin)**: Pipe content to the command's standard input.
+- **Working Directory**: Specify the directory to execute the command in.
+- **Timeout**: Configurable timeout (default 300s) with process group killing.
+- **Standard Exit Codes**: Returns 124 for timeout, 128+N for signals.
+- **Output Guard**: Caps output size to 1MB to prevent memory issues.
+
+## Tools
+
+### `run-command`
+
+Executes a shell command or script.
+
+#### Parameters
+
+- `command` (string, required): The shell command or script to execute.
+- `args` (array of strings, optional): Arguments passed to the script.
+- `env` (object, optional): Environment variables to set.
+- `cwd` (string, optional): The directory to run the command in.
+- `timeout` (number, optional): Timeout in seconds (default: 300).
+- `stdin` (string, optional): Content to pass to standard input.
+
+#### Output
+
+- `stdout` (string): Standard output (truncated at 1MB).
+- `stderr` (string): Standard error (truncated at 1MB).
+- `exitCode` (number): The exit code.
+  - `0`: Success.
+  - `1-123`: Command failure.
+  - `124`: Timeout.
+  - `128+N`: Terminated by signal N (e.g. 143 for SIGTERM).
+- `timedOut` (boolean): True if the process was terminated due to timeout.
+
+## Examples
+
+### Simple Command
+
+```json
+{
+  "name": "run-command",
+  "arguments": {
+    "command": "ls -la"
+  }
+}
+```
+
+### With Arguments
+
+```json
+{
+  "name": "run-command",
+  "arguments": {
+    "command": "echo Hello $1",
+    "args": ["World"]
+  }
+}
+```
+
+### With Environment Variables
+
+```json
+{
+  "name": "run-command",
+  "arguments": {
+    "command": "echo $MY_VAR",
+    "env": { "MY_VAR": "secret" }
+  }
+}
+```
+
+### With Stdin
+
+```json
+{
+  "name": "run-command",
+  "arguments": {
+    "command": "grep foo",
+    "stdin": "bar\nfoo\nbaz"
+  }
+}
+```
+
+### With Timeout
+
+```json
+{
+  "name": "run-command",
+  "arguments": {
+    "command": "sleep 10",
+    "timeout": 2
+  }
+}
+```
+
+## Testing
+
+You can test this server using the
+[MCP Inspector](https://github.com/modelcontextprotocol/inspector).
+
+1. Build the server: `npm install && npm run build`
+2. Run with inspector: `npx @modelcontextprotocol/inspector node dist/index.js`