CI, added some memories

.github/workflows/pytest.yml

@@ -55,9 +55,4 @@ jobs:
         run: uv pip install -e ".[dev]"
       - name: Test with pytest
         shell: bash
-        run: |
-          if [ "${{ runner.os }}" = "Linux" ]; then
-            uv run pytest -vv -m "not java and not rust"
-          else
-            uv run pytest -vv
-          fi
+        run: uv run poe test

.serena/memories/deadlock_analysis_mcp_symbolic_tools.md

@@ -0,0 +1,63 @@
+# Deadlock Analysis: MCP Symbolic Tools Timeout Issue
+
+## Problem Summary
+Intermittent deadlocks occur when using symbolic tools (particularly `find_symbol`) through MCP clients. Successful calls are followed by calls that hang for 240 seconds before timing out. Once a timeout occurs, the language server calls will no longer respond.
+
+## ROOT CAUSE DISCOVERED: Asyncio Event Loop Interference
+
+### Critical Evidence from MCP Server Logs
+The smoking gun was found in the MCP server logs showing **unawaited coroutines**:
+
+```
+INFO mcp.server.lowlevel.server:_handle_message:524 - Warning: RuntimeWarning: coroutine 'LanguageServer.request_full_symbol_tree' was never awaited
+```
+
+This warning is being logged by the **MCP server's `_handle_message` method**, not SerenaAgent code, indicating coroutines are being created in the MCP server's asyncio context but never properly awaited.
+
+### The Real Issue: Dual Asyncio Context Contamination
+
+**Architecture Problem:**
+1. **MCP Server**: Runs its own asyncio event loop to handle incoming requests
+2. **SerenaAgent**: Creates its own asyncio event loop in separate thread for language serve, and even a second loop for the dashboard if so configured
+3. **Conflict**: When MCP server calls SerenaAgent tools, we have **two or three asyncio contexts interacting**
+
+**Deadlock Mechanism:**
+```
+MCP Server (asyncio loop A) 
+  → handles tool request 
+  → calls SerenaAgent.find_symbol()
+  → SerenaAgent uses asyncio.run_coroutine_threadsafe()
+  → Creates coroutine in language server loop (loop B)
+  → BUT: Coroutine gets leaked into MCP's context and never awaited
+  → Dangling coroutines accumulate in MCP server's loop
+  → Eventually causes resource exhaustion/event loop blocking
+  → Language server appears to "hang" but it's actually MCP loop contamination
+```
+
+### Discarded Hypotheses
+- **Not a timeout issue**: Language server actually works fine in isolation
+- **Not abandoned threads**: The threading mechanism works correctly
+- **Not LSP deadlock**: The TypeScript language server itself isn't hanging
+
+The actual issue is **asyncio context bleeding** between MCP server and SerenaAgent.
+
+### Why We Can't Reproduce Outside MCP
+- **Direct script calls**: No MCP server, no dual asyncio context
+- **Single event loop**: Only SerenaAgent's language server loop exists  
+- **No async interference**: Clean, isolated execution
+- **MCP-specific**: Requires the exact async context interaction pattern
+
+## Technical Details
+
+### Key Files and Locations
+- `src/multilspy/language_server.py:1870` - `run_coroutine_threadsafe` creates coroutines that leak to MCP context
+- MCP server `_handle_message` - Where unawaited coroutine warnings appear
+
+## Solution
+**Process Isolation** is the fundamental fix:
+1. **Separate processes**: MCP server, SerenaAgent and Dashboard in different processes
+2. **IPC communication**: Replace direct method calls with inter-process communication
+3. **Clean async boundaries**: Each process manages its own asyncio context
+4. **No coroutine leakage**: Complete isolation prevents context contamination
+
+This explains why the deadlock is **MCP-specific** and doesn't occur in direct tool execution - it's fundamentally about asyncio context contamination between the MCP server and SerenaAgent.

.serena/memories/suggested_commands.md

@@ -4,10 +4,24 @@
 
 The following tasks should generally be executed using `uv run poe <task_name>`.
 
-- `lint`: This is the **only** allowed command for linting. Run as `uv run poe lint`.
 - `format`: This is the **only** allowed command for formatting. Run as `uv run poe format`.
 - `type-check`: This is the **only** allowed command for type checking. Run as `uv run poe type-check`.
-- `test`: This is the preferred command for running tests (`uv run poe test [args]`). However, running tests directly with `uv run pytest [args]` is also permitted.
+- `test`: This is the preferred command for running tests (`uv run poe test [args]`). You can select subsets of tests with markers,
+   the current markers are
+   ```toml
+    markers = [
+        "python: language server running for Python",
+        "go: language server running for Go",
+        "java: language server running for Java",
+        "rust: language server running for Rust",
+        "typescript: language server running for TypeScript",
+        "php: language server running for PHP",
+        "snapshot: snapshot tests for symbolic editing operations",
+        "isolated_process: test runs with process isolated agent",
+    ]
+   ```
+  By default, `uv run poe test` uses the markes set in the env var `PYTEST_MARKERS`, or, if it unset, uses `-m "not java and not rust and not isolated process"`.
+  You can override this behavior by simply passing the `-m` option to `uv run poe test`, e.g. `uv run poe test -m "python or go"`.
 
 For finishing a task, make sure format, type-check and test pass! Run them at the end of the task
 and if needed fix any issues that come up and run them again until they pass.

pyproject.toml

@@ -106,9 +106,10 @@ exclude = "^build/|^docs/"
 PYDEVD_DISABLE_FILE_VALIDATION = "1"
 
 [tool.poe.tasks]
-# Uses PYTEST_MARKERS env var for default markers (defaults to "not java and not rust")
-# Set PYTEST_MARKERS="" to run all tests
-test = "pytest test --color=yes -m \"${PYTEST_MARKERS:-not java and not rust}\""
+# Uses PYTEST_MARKERS env var for default markers
+# For custom markers, one can either adjust the env var or just use -m option in the command line,
+# as the second -m option will override the first one.
+test = "pytest test -vv -m \"${PYTEST_MARKERS:-not java and not rust and not isolated process}\""
 _black_check = "black --check --exclude src/multilspy/ src scripts test"
 _ruff_check = "ruff check --exclude .venv/ --exclude src/multilspy/ src scripts test"
 _black_format = "black --exclude .venv/|src/multilspy/ src scripts test"
@@ -259,6 +260,6 @@ markers = [
     "rust: language server running for Rust",
     "typescript: language server running for TypeScript",
     "php: language server running for PHP",
-    "snapshot: snapshot tests",
+    "snapshot: snapshot tests for symbolic editing operations",
     "isolated_process: test runs with process isolated agent",
 ]