When using the connection parameters trustStore and keyStore until Version 1.5.4, it was possible to specifiy values in java.net.URL-syntax. To read the files via InputStream, org.mariadb.jdbc.internal.protocol.AbstractConnectProtocol and org.mariadb.jdbc.internal.protocol.tls.MariaDbX509TrustManager used code like this:
inStream = new URL(keyStoreUrl).openStream();
Since Version 1.5.5, the constructor java.io.FileInputStream(String) is used to create the java.io.InputStream, the consequence being that trustStore and keyStore have to point to a file in the file system. Before version 1.5.5 it was possible to point to a file in a jar for example, because the URL's protocol would be used.
Do you see any chance to support a behaviour similar to the older versions? An interesting use case for this might be, that you could build a module for data access, which encapsulated functionality to build a project specific connection string, say for a number of different databases. This module would also include JKS stores and would be distributed as a jar.
In general, I think it should not be necessary to keep resources as plain files in the file system.