Java: Move away from deprecated HTTP client API after libraries update.
Java: Updating IntelliJ settings to Java 7 and correct the name of libraries files.
Remove warnings from several Java source files.
Remove a FIXME comment that no longer applies.

This comment was referring to curlpp, which we no longer use.
Avoid the dependency on the makefile from Go.

This avoids the extra step of "make golibs", and also leaves Go in control of
compilation flags.
Minor cleanups in the proto files.
Merge pull request #17 from eranmes/idea_fix

Java: Follow-up on httpclient & httpcore libraries update by moving away from deprecated HTTP client API and updating IntelliJ settings.
Clean up #include ordering and add missing ones.

Make sure any header that has a corresponding .cc file includes that header
first, to validate that it can stand by itself (as per the style guide). Also
do some simple reformatting (mainly sorting "using" statements, or moving
them to the location prescribed by the style guide).
Add a .md extension to go/README.
Update the content of go/README.md to Markdown.
Convert go/README to Markdown format.
Remove the nearly useless go/ENV file.
Reformat merkle_tree_go.cc.