gen_compile_commands.py: fix path resolve with symlinks in it

When a path contains relative symbolic links, os.path.abspath() might
not follow the symlinks and instead return the absolute path with just
the relative paths resolved, resulting in an incorrect path.

1. Say "drivers/hdf/" has some symlinks:

    # ls -l drivers/hdf/
    total 364
    drwxrwxr-x 2 ...   4096 ... evdev
    lrwxrwxrwx 1 ...     44 ... framework -> ../../../../../../drivers/hdf_core/framework
    -rw-rw-r-- 1 ... 359010 ... hdf_macro_test.h
    lrwxrwxrwx 1 ...     55 ... inner_api -> ../../../../../../drivers/hdf_core/interfaces/inner_api
    lrwxrwxrwx 1 ...     53 ... khdf -> ../../../../../../drivers/hdf_core/adapter/khdf/linux
    -rw-r--r-- 1 ...     74 ... Makefile
    drwxrwxr-x 3 ...   4096 ... wifi

2. One .cmd file records that:

    # head -1 ./framework/core/manager/src/.devmgr_service.o.cmd
    cmd_drivers/hdf/khdf/manager/../../../../framework/core/manager/src/devmgr_service.o := ... \
    /path/to/src/drivers/hdf...