Look more carefully at what you've written
export CFLAGS="-I $HOME/.swish/include"; overwrites
export CFLAGS="-I $HOME/.gsl/include"; which overwrites
export CFLAGS="-I $HOME/.libstree/include";
and the LDFLAGS code is similar
LD_LIBRARY_PATH is different, each time you set it you are including its previous value, extending it rather than overwriting it:
export LD_LIBRARY_PATH=/home/ewijaya/MyBioTool/libstree-0.4.2/lib:${LD_LIBRARY_PATH}
To simplify, try something like:
export CFLAGS="-I $HOME/.swish/include:$HOME/.gsl/include:$HOME/.libstree/include";
hope this helps