This commit essentially ensures before writing .blend file that only
actualy locally used linked IDs are tagged as LIB_TAG_EXTERN (and
therefore get a reference stored in the .blend file).

Previously, a linked ID tagged as directly linked would never get back
to the indirectly linked status. Consequence was a lot of 'needless'
references to linked data in .blend files.

This commit also introduces a new flag for lib_query ID usage types,
IDWALK_CB_DIRECT_WEAK_LINK, used currently for base's Object
pointer, and for LayerCollection's Collection pointer.

Overhead of new process is below 0.1% in whole file saving process in
a Heist production file e.g.

Note that timing debug code will be cleaned up before commit.