Moving C++ code to its own subdirectory, adding a top-level Makefile that is
separate from the C++ one.
Fixing IntelliJ repository directory mapping.
Java: Expose warnings when building from the command line.
Organize and sort the .gitignore entries.
Fix up a number of .gitignore entries.

Most of these were caused by c41b090.
Switch to using an iterator to avoid raw types / unchecked conversion warnings.
Upgrade libraries:
 - httpclient from 4.2.5 to 4.3.3
 - httpcore from 4.2.4 to 4.3.2

Both changes will be used in a later commit to add CT log retrieve
functionality to the Java client.
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.
Use the protobuf jar file from the system.

Either sysjarsdir or jars.protobuf can be overridden in local.properties.
Add support for a basic Travis continuous build.

Their environment is based on Ubuntu Precise, missing a number of necessary
packages, so this is only the subset that builds right off (Java and the
"pure Go").
Improve the Go binding for merkletree.
Run the Python tests on our continuous build.
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.
Move out the existing makefile.
First cut at autotools.