pear: add options for bin_dir, php_bin, and php_dir settings

packages with executables will put their bins in bin_dir, which is
prefix/pear by default. php_bin can be used if the php interpreter is
in a different location on the target system. php_dir can be used for
overriding the directory where php files are put (useful on debian).
pear: remove debug statement
pear: add more unnecessary pear directories to delete
pear: replace pear_path in executable files

some packages put the pear_path value in their executable (PHPUnit for example)
which is the staging path, so it has to be replaced to the installed path, otherwise
the executable won't work