Den konvention, jeg bruger, og jeg har set i de fleste open source-projekter (inklusive Spring et al), er at placere alle ikke-java-filer under en ressourcemappe, under en beskrivende mappe:
module-root/
src/
main/
java/
(Java sources go here)
resources/
log4j.xml
spring/ (spring xmls go here)
sql/ (sql scripts go here)
mongo/ (<-- seems like a good place for mongoDB functions)
test/
unit/
java/ (unit test java sources go here)
resources/ (unit test specific resources - usually none)
integration/
java/ (integration test java sources go here)
resources/
spring/ (usually an ITestAssembly.xml goes here)
Bygfilen pakker derefter ressourcerne i en ressource-jar, som bliver implementeret sammen med alle de andre jars.