Fix make cleanall && make

[tkelman]

since cleanall was deleting shlibdir but not manifest,
was unable to link suitesparse_wrapper against cholmod etc

the buildbots have not been very happy, see e.g. https://build.julialang.org/builders/build_ubuntu14.04-x64/builds/1405/steps/shell_1/logs/stdio

[staticfloat]

This seems pretty straightforward; going to merge it so that the buildbots can continue spitting out binaries. The takeaway from this is that there is now no difference between cleanall and distclean for the julia build; the only difference is for dependencies.

[tkelman]

right. the previous make cleanall would force all deps to redo their install because the shared libs were used as the makefile dependencies. now that's no longer the case, deleting the shared libs doesn't trigger anything as far as make is concerned. not ideal imo.

an alternative to deleting the whole prefix here would be running uninstall for all the deps, but i don't trust that to be fully working yet.

[staticfloat]

This is due to the new manifest files that make depends on, right? @vtjnash, I believe you were the one to make this change recently, could you give us an idea on how these manifest files are supposed to deal with a situation like this? Is the "proper" answer to delete the manifest files to force the reinstallation of libraries? What benefit do these manifest files have over simply relying on the libraries themselves? It seems to me that this will make it very easy for devs to delete a shared library, expecting it to be reinstalled when they run make again, then being surprised when the files are not installed again.

[vtjnash]

Yeah, now you could just delete manifest/dep instead of trying to guess the random correct library file to delete to get it to reinstall. Or you can just remove all of usr (install is fast now). Or you can run make -C deps reinstall-dep.

We could even put the total set of installed files into the manifest file and check manually in the makefile to check that none are missing.

[staticfloat]

We could even put the total set of installed files into the manifest file and check manually in the makefile to check that none are missing.

I think that is important, because make should "just work". Especially if I've somehow deleted a library, I don't remember which one, and I want to run make to build everything again.