I am using GIT integrated with Domino designer(version 9.0.1). I have associated a .nsf project to an on-disk project. I have synced this on-disk project with my source control repository. This seems to be the way of doing things. But the on-disk project doesn't have the Java classes and packages I had in my .nsf project under "Local" directory. So how could I possibly sync these files and packages also?
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The "Local" directory doesn't get stored in on-disk project. It is used by Domino designer internally to e.g. create Java classes from XPages. As those classes are build and updated automatically during project build there is no need to save them in on-disk project for source control reasons.
Store your Java classes and packages somewhere else in .nsf. The classic way (compatible with 8.5.x versions) is to put them into Design Code element "Java" folder "Code/Java" or "src" (Java classes), "res" (resources/property files) and "WebContent/Web-INF/bin" (jar files). Since version 9 you can put your jar files into Design Code element "Jars".

Knut Herrmann
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Also note: The "Local" folder in the nsf is NOT actually in the nsf. It is in the WorkSpace folder on the developers local machine. This is the main reason you should not do team development against the same NSF on a server. You end up with out of sync Local files. – Newbs Jun 10 '14 at 13:27
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@Newbs, Thanks for the heads up on "Local" folder. And yes, I maintain a local .nsf project that is associated with, an on-disk project which is under source control. We developers work on our local nsf projects and finally push changes when necessary to the on-disk project. – user3484371 Jun 11 '14 at 04:51
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@Knut Herrmann. Thanks that worked. I placed all my Java packages and class under Code/Java and they appeared in the on-disk project. – user3484371 Jun 11 '14 at 05:12