Clean includes

[kkhoot]

This PR reduces header includes to speed up (partial) builds.

1. Give appropriate subcategory layer headers to each layer/test file.
   Most of the layers/tests include the monolithic header vision_layers.hpp which causes recompiling almost all layer/test cpps when changes in other subcategory layer headers (such as common_layers.hpp, etc.) are made.
2. Remove unnecessary headers
   Many of the files include unneeded headers (such as cstring). Most of these includes were erased.

-During this work, I found that HDF5 defines are defined in a different layer header, so moved it to the right place.

[ronghanghu]

@kkhoot Thanks for the header cleanup! I'll try to review tonight or tomorrow.

[ronghanghu]

The headers seem much cleaner after this PR. Thanks again @kkhoot

[shelhamer]

Thanks for this @kkhoot. This is a nice reform and a step in the direction of #1646.

[kkhoot]

@ronghanghu @shelhamer Thanks for quick review :)