I was able to reproduce those errors. However, instead of completely deleting 
Makefile.in, 
Makefile.am, and 
aclocal.m4, I just updated their time-stamps (as suggested here 
http://stackoverflow.com/a/33279062/1675668) using 
touch with the following command:
touch aclocal.m4 configure Makefile.am Makefile.in
Hunspell is a dependency so I just installed it using HomeBrew. For wxWidgets, I did not use the one through HomeBrew, but instead built it myself on 10.12 Sierra (wxWidgets-3.0.3).
Error #1 (use of overloaded operator '==' is ambiguous)Trying to build using 
make reports 4 warnings, 1 error when attempting to compile 
$(CB_ROOT)/src/plugins/debuggergdb/debuggergdb.cpp. The specific error:
In file included from debuggergdb.cpp:10:
In file included from ../../../src/include/sdk.h:17:
In file included from ../../../src/include/sdk_precomp.h:13:
In file included from ../../../src/include/sdk_common.h:43:
../../../src/include/prep.h:33:75: error: use of overloaded operator '==' is ambiguous (with operand types 'const std::__1::shared_ptr<GDBWatch>' and 'int')
        template<typename T> bool equals(T const& rhs) const { return rhs == 0; }
                                                                      ~~~ ^  ~
This error has actually been encountered before on this forum:
../../../../src/include/prep.h:33:75: error: use of overloaded operator '==' is ambiguous (with operand types 'const std::__1::shared_ptr<GDBWatch>' and 'int')
        template<typename T> bool equals(T const& rhs) const { return rhs == 0; }
                                                                      ~~~ ^  ~
The suggestion was to add 
CXXFLAGS="-stdlib=libc++". I had previously used this solution to build wxWidgets (since I did not use HomeBrew) and I instead used 
CXXFLAGS="-stdlib=libc++ -std=c++" LDFLAGS="-stdlib=libc++" so I used the latter for configuring the build of Code::Blocks. My configure command looked like: 
./configure --with-contrib-plugins=all CXXFLAGS="-stdlib=libc++ -std=c++11" LDFLAGS="-stdlib=libc++"
Attempting to 
make again results in another error:
In file included from directorymonitor.cpp:3:
In file included from ./se_globals.h:10:
In file included from ../../../../src/include/sdk.h:17:
In file included from ../../../../src/include/sdk_precomp.h:13:
In file included from ../../../../src/include/sdk_common.h:150:
In file included from ../../../../src/include/filemanager.h:13:
../../../../src/include/backgroundthread.h:143:13: warning: 'this' pointer cannot be null in well-defined C++ code; pointer may be assumed to always convert to true [-Wundefined-bool-conversion]
        if (this && IsRunning())
            ^~~~ ~~
directorymonitor.cpp:27:10: fatal error: 'fam.h' file not found
#include <fam.h> //USES EITHER GAMIN OR FAM (IDENTICAL FILE MONITORING APIS)
         ^
3 warnings and 1 error generated.
This issue had also been encountered previously and was solved by ommiting a couple plugins:
Ok, so I managed to move forward in the compile process by leaving out a couple of plugins...
-FileManager,-NassiShneiderman
So the configure command turned into: 
./configure --with-contrib-plugins=all,-FileManager,-NassiShneiderman CXXFLAGS="-stdlib=libc++ -std=c++11" LDFLAGS="-stdlib=libc++"
Running 
make one last time after the above 
configure ran without a hitch. The last step was to run 
make install to move the binary into 
/usr/local/bin.
 Missing Plugins (and maybe other components)
Missing Plugins (and maybe other components)Unfortunately, the plugins do not work. Running 
codeblocks in the shell to open up the IDE reveals that it gets stuck when initializing plugins; opening up the plugin manager reveals no plugins loaded.

So although the interface is up and running, some components are missing 

 Maybe I missed something in the build configuration?