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Cherokee development sources are in its own subversion repository, you can read instructions at Subversion Repository Instructions.
Cherokee do not support .htaccess files. You can do directory configuration into the main site configuration file, see the Directory_configuration
Cherokee is small and high performant server, then if you need to listen different TCP ports the best way is to start different cherokee web servers. You do not need two cherokee's binary files and you can use different configuration files, like this example:
# cherokee -b -C cherokee80.cfg # cherokee -b -C cherokeePORT-B.cfg
Most of the Cherokee Web Server code is on shared libraries. It will help the system to save some memory by sharing that code.
If you are trying to use the PAM validator and you are getting an error, it might be because you did not compile it. You can test it looking for the libplugin_pam.so on the plug-in path (usually /usr/lib/cherokee/).
So, if you want to recompile Cherokee in order to get the PAM module working, ensure you have the PAM development package installed on your system.