Make it clear that JARs get local/root and git/url content

[seancorfield]

Right now this is only mentioned under AOT compilation, but it should be more prominent since it affects library JARs as well. It should recommend using :exclude to stop such sources being included.

[seancorfield]

I've updated the README but it would be a good idea to look at exactly what this looks like in practice and whether it would be worth having an option to only include paths, rather than local/git deps? Now that we compute the project basis, that is probably more tenable (we could use just :paths instead of the classpath, perhaps, for libraries?).

[seancorfield]

Added new :paths-only option. For backward compatibility, it is false even for library JAR files.