Howdy -- please see the following example:
=== expath-pkg.xml
<?xml version="1.0"?>
  <title>Namespace Trouble Test</title>
  <xquery>
    <file>foo.xq</file>
  </xquery>
  <xquery>
    <file>bar.xq</file>
  </xquery>
</package>
=== ns-test/foo.xq
declare function foo:test() {
  1 + 1
 };
=== ns-test/bar.xq
declare function bar:test() {
  1 + 1
 };
=== ...in the basex-gui buffer...
=== ...results in...