Commit only property changes on root of repo, not files

Solution 1:

In order to commit only the explicit paths specified on the command line use the --depth empty option e.g. in the directory with the newly modified externals property:

$svn commit --depth empty . -m "Modify svn externals definition only."

Solution 2:

If you only want to change the property you can do it against the repository right away, instead of against your working copy.

For example:

svn propset svn:externals "test http://yourhost.com/svn/trunk/module/test/src" --revprop -r HEAD http://yourhost.com/svn/trunk/module

See the SVN book on manipulating properties