1. Clean up clk usage in IDF, replace rtc_clk_xtal/apb_freq_get with
upper level API esp_clk_xtal/apb_freq
2. Fix small errors and wrong comments related to clock
3. Add clk_tree_defs.h to provide an unified clock id for each chip
Modify the NGed drivers to adopt new clock ids
This commit updates the visibility of various header files and cleans up
some unnecessary inclusions. Also, this commit removes certain header
include paths which were maintained for backward compatibility.