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I can imagine you don't want the 'remove generated files' commit - although I consider it very bad practice to put generated files in a git repository; I had to re-run aclocal -m m4; autoheader; autoconf; automake --missing --foreign anyway because you used am version 1.14 to generate these files, which I don't have installed; which breaks building.
Removing 'using namespace std' and using the correct standard header names are just good C++ practice. You should probably merge those. The compiler warning thing is just a warning, but compiler warnings are annoying. Finally, if you'd be so kind to consider adding cwm4 support then I don't need to keep my own fork ;). This just adds a file configure.m4 which then allows fully automatic integration with other projects (that use cwm4) as git submodule (no configuration or editing of build system files required: just a git submodule add ... and done).