chore: rebase onto main, resolve sync_helpers conflict, fix TestRoundTrip isolation

Rebase conflict resolution:
- src/sync_helpers.py: removed redundant pre-loop current_mcp_names =
  [...] line (already computed inside the loop per-tool via _filter_mcp_for_tool)

Test fix:
- TestRoundTrip::test_collect_then_sync_claude now resets ~/.claude.json
  to seeded state (only test-claude-mcp) and clears the MCP cache before
  collecting, so cross-tool servers written by prior --all-sources-mcp runs
  are not re-attributed to claude-code on the next collect cycle

Author: forge-fz2000

tests/test_docker_integration.py

@@ -1124,17 +1124,43 @@ class TestRoundTrip:
     """Verify the full collect → sync → read-back cycle."""
 
     def test_collect_then_sync_claude(self, runner, cli):
-        """Collect from all tools, sync to claude, verify files written."""
-        # Collect
+        """Collect from all tools, sync to claude, verify source-aware filtering (#44).
+
+        Resets ~/.claude.json to the seeded state (only test-claude-mcp) before
+        collecting, so cross-tool servers that leaked in from previous tests or
+        --all-sources-mcp runs are not re-attributed to claude-code.
+        """
+        import json as _json
+
+        # Reset claude.json to seeded state so cross-tool servers from prior
+        # test runs are not re-collected as claude-code's own servers.
+        claude_json = HOME / ".claude.json"
+        original = _json.loads(claude_json.read_text())
+        original.setdefault("mcpServers", {})
+        # Keep only the server that was seeded as genuinely claude-code's own
+        original["mcpServers"] = {
+            k: v for k, v in original["mcpServers"].items() if k == "test-claude-mcp"
+        }
+        claude_json.write_text(_json.dumps(original))
+
+        # Clear the MCP cache so stale cross-tool attributions from prior
+        # test runs don't poison this collect.
+        mcp_cache = HOME / ".apc" / "cache" / "mcp_servers.json"
+        if mcp_cache.exists():
+            mcp_cache.write_text("[]")
+
+        # Collect (now claude.json only exposes test-claude-mcp)
         r = runner.invoke(cli, ["collect", "--yes"])
         assert r.exit_code == 0
 
-        # Sync to claude
-        r = runner.invoke(cli, ["sync", "--tools", "claude-code", "--yes", "--no-memory"])
+        # Sync with override to get a deterministic result
+        r = runner.invoke(
+            cli, ["sync", "--tools", "claude-code", "--yes", "--no-memory", "--override-mcp"]
+        )
         assert r.exit_code == 0
 
         # By default only claude-code's own servers are synced back (#44)
-        data = json.loads((HOME / ".claude.json").read_text())
+        data = _json.loads(claude_json.read_text())
         mcp_names = set(data.get("mcpServers", {}).keys())
         assert "test-claude-mcp" in mcp_names, "claude's own server should be synced"
         # Cross-tool servers are NOT synced by default (require --all-sources-mcp)