Address PR #27 review feedback: path normalization, tests, and conventions (#28)

* Initial plan

* Fix import ordering, restore dot prefix, normalize temp dir paths, add unit tests

Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

* Remove weak test case and document limitation in comment

Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Author: Copilot

server/dist/codeql-development-mcp-server.js

@@ -9,9 +9,9 @@ import { setTimeout, clearTimeout } from 'timers';
 import { pathToFileURL } from 'url';
 import { delimiter, join } from 'path';
 import { logger } from '../utils/logger';
+import { getPackageVersion } from '../utils/package-paths';
 import { getProjectTmpDir } from '../utils/temp-dir';
 import { getResolvedCodeQLDir } from './cli-executor';
-import { getPackageVersion } from '../utils/package-paths';
 
 export interface LSPMessage {
   jsonrpc: '2.0';

server/dist/codeql-development-mcp-server.js.map

@@ -403,6 +403,6 @@ function parseBoolEnv(envVar: string | undefined, defaultValue: boolean): boolea
 
 // Export singleton instance with environment variable support
 export const sessionDataManager = new SessionDataManager({
-  storageLocation: process.env.MONITORING_STORAGE_LOCATION || join(getProjectTmpBase(), 'ql-mcp-tracking'),
+  storageLocation: process.env.MONITORING_STORAGE_LOCATION || join(getProjectTmpBase(), '.ql-mcp-tracking'),
   enableMonitoringTools: parseBoolEnv(process.env.ENABLE_MONITORING_TOOLS, false),
 });

server/src/lib/language-server.ts

@@ -8,7 +8,7 @@
  */
 
 import { mkdirSync, mkdtempSync } from 'fs';
-import { join } from 'path';
+import { isAbsolute, join, resolve } from 'path';
 import { getPackageRootDir } from './package-paths';
 
 /**
@@ -17,10 +17,14 @@ import { getPackageRootDir } from './package-paths';
  * Resolution order:
  * 1. `CODEQL_MCP_TMP_DIR` environment variable — for read-only package root
  *    scenarios (e.g., npm global installs where the package directory is not
- *    writable).
+ *    writable). Relative paths are resolved against process.cwd().
  * 2. `<packageRoot>/.tmp` — default; excluded from version control.
  */
-const PROJECT_TMP_BASE = process.env.CODEQL_MCP_TMP_DIR || join(getPackageRootDir(), '.tmp');
+const PROJECT_TMP_BASE = process.env.CODEQL_MCP_TMP_DIR
+  ? (isAbsolute(process.env.CODEQL_MCP_TMP_DIR) 
+      ? process.env.CODEQL_MCP_TMP_DIR 
+      : resolve(process.cwd(), process.env.CODEQL_MCP_TMP_DIR))
+  : join(getPackageRootDir(), '.tmp');
 
 /**
  * Return the project-local `.tmp` base directory, creating it if needed.

server/src/lib/session-data-manager.ts

@@ -571,6 +571,109 @@ describe('registerCLITool handler behavior', () => {
     );
   });
 
+  it('should resolve relative tests parameter against user workspace dir', async () => {
+    const definition: CLIToolDefinition = {
+      name: 'codeql_test_run',
+      description: 'Run tests',
+      command: 'codeql',
+      subcommand: 'test run',
+      inputSchema: {
+        tests: z.array(z.string())
+      }
+    };
+
+    registerCLITool(mockServer, definition);
+    
+    const handler = (mockServer.tool as ReturnType<typeof vi.fn>).mock.calls[0][3];
+    
+    executeCodeQLCommand.mockResolvedValueOnce({
+      stdout: 'All tests passed',
+      stderr: '',
+      success: true
+    });
+
+    // Test with relative paths
+    await handler({ tests: ['relative/test1.ql', '/absolute/test2.ql'] });
+
+    // executeCodeQLCommand signature: (subcommand, options, additionalArgs, cwd)
+    const call = executeCodeQLCommand.mock.calls[0];
+    const positionalArgs = call[2];
+    
+    // First relative path should be resolved to absolute
+    expect(positionalArgs[0]).not.toBe('relative/test1.ql');
+    expect(positionalArgs[0]).toContain('relative/test1.ql');
+    
+    // Second absolute path should remain unchanged
+    expect(positionalArgs[1]).toBe('/absolute/test2.ql');
+  });
+
+  it('should resolve relative database parameter against user workspace dir', async () => {
+    const definition: CLIToolDefinition = {
+      name: 'codeql_query_run',
+      description: 'Run query',
+      command: 'codeql',
+      subcommand: 'query run',
+      inputSchema: {
+        database: z.string(),
+        query: z.string()
+      }
+    };
+
+    registerCLITool(mockServer, definition);
+    
+    const handler = (mockServer.tool as ReturnType<typeof vi.fn>).mock.calls[0][3];
+    
+    executeCodeQLCommand.mockResolvedValueOnce({
+      stdout: '{"columns":[]}',
+      stderr: '',
+      success: true
+    });
+
+    // Test with relative database path
+    await handler({ database: 'my-database', query: '/path/to/query.ql' });
+
+    // executeCodeQLCommand signature: (subcommand, options, additionalArgs, cwd)
+    const call = executeCodeQLCommand.mock.calls[0];
+    const options = call[1];
+    
+    // Relative database path should be resolved to absolute
+    expect(options.database).not.toBe('my-database');
+    expect(options.database).toContain('my-database');
+  });
+
+  it('should resolve relative dir/packDir parameter against user workspace dir', async () => {
+    const definition: CLIToolDefinition = {
+      name: 'codeql_pack_install',
+      description: 'Install packs',
+      command: 'codeql',
+      subcommand: 'pack install',
+      inputSchema: {
+        dir: z.string()
+      }
+    };
+
+    registerCLITool(mockServer, definition);
+    
+    const handler = (mockServer.tool as ReturnType<typeof vi.fn>).mock.calls[0][3];
+    
+    executeCodeQLCommand.mockResolvedValueOnce({
+      stdout: 'Installed successfully',
+      stderr: '',
+      success: true
+    });
+
+    // Test with relative dir path
+    await handler({ dir: 'my-pack-dir' });
+
+    // executeCodeQLCommand signature: (subcommand, options, additionalArgs, cwd)
+    const call = executeCodeQLCommand.mock.calls[0];
+    const cwd = call[3];
+    
+    // Relative dir should be resolved to absolute for cwd
+    expect(cwd).not.toBe('my-pack-dir');
+    expect(cwd).toContain('my-pack-dir');
+  });
+
   it('should handle dir parameter as positional for pack_ls', async () => {
     const definition: CLIToolDefinition = {
       name: 'codeql_pack_ls',