When porting non-ixemul software check file system paths and path handling. Often *nix path handling is used what is incompatible with Amiga path handling.
AOS4 SDK and AROS SDKs has a Bash port and a set of Unix like commands, but there will be some issues with expected paths etc.
* Setting up GeekGadgets
MorphOS SDK provides GeekGadgets development environment including Bash port and required build tools (automake etc.). To port software you usually start by running configure script from MorphOS shell and then executing make.
Ixemul is convenient method to port development tools from Linux. Using ixemul is not recommended for user applications and ixemul software is always intended to be used in GeekGadgets environment.
AOS4 has a partial(?) pthread implementation. For older AOS, and for AROS you need to wrap the Amiga specific calls yourself (is this correct?). MorphOS provides pthreads implementation but using native Amiga API is recommended as pthreads can not be securely implemented on Amiga.