added some eclipse products to the gitignore
Changing the directory structure of SCAPI so that it will be more friendly
to the Open source community. This is the first of several commits regarding the dir structure.

changes made:
1) removed the Code/ directory, instead:
- the java code of scapi sits under src/java/
- the jni (c++) source code sits under src/jni/

2) changed the Docs/ dir to doc/ and moved the UML/ dir under doc/

3) removed all external libraries from the repository, instead:
the external libraries are now git submodules that sit under lib/
edited the jni crypto pp interface code so it can be compiled on *nix based operating systems.
also added a makefile for linux.
migrated the ntl jni interface to linux and added a makefile
migrated the otextension jni interface to linux and added a makefile
changed the directory name of JniOtExtension
fixed a few issues (such as incorrect types) during linux migration
migrated the openssl jni interface to linux and added new source files to makefile
renamed the openssl jni interface dir
migrated the miracl jni interface to linux, added a makefile and scripts that helps to compile miracl
1) added a few more exceptions to gitignore
2) rewritten the jni crypto++ makefile
3) started a main makefile for scapi that currently can compile crypto++ and its jni interface.
- added the build directory (used as compilation staging dir)
- added a MiraclCompilation dir with a general makefile and specialized mirdef.h files
- refactored the makefile of the miracl jni interface
- added a few miracl related rules to the main makefile
- fixed some bugs in the makefiles
- removed obsolete miracl_compilation dir from MiraclJavaInteface dir
(we now have instead lib/MiraclCompilation/)
added make rules for openssl, fixed a few rules for miracl, cryptopp
removed submodule OTExtension
added again our own fork of OTExtension as submodule
added jni-otextension to main makefile
added compile-bouncycastle to makefile
added ntl target, moved everything to build dir
1) added marker files (compile-*) for the makefile so that it won't recompile unnecessary targets
2) added the marker files and build/ dir to the gitignore file
3) fixed a bug in the ntl makefile