You IDE is "helping" you put resources into the classpath.
When running maven clean the entire target/ directory is removed, so if things exist otherwise, it is because someone else copies into it.
Resources in maven usually goes in src/main/resources or src/test/resources unless otherwise configured. Your xml file is probably in a src/main/java or src/test/java folder, and therefore being copied by the IDE.
If you want to have resources inside your java folders, a helpful answer is this one:
In maven how can I include non-java src files in the same place in the output jar?