repository: move 'repository_format_precious_objects' to repo scope

repository: move 'repository_format_precious_objects' to repo scope

The 'extensions.preciousObjects' setting when set true, prevents
operations that might drop objects from the object storage. This setting
is populated in the global variable
'repository_format_precious_objects'.

Move this global variable to repo scope by adding it to 'struct
repository and also refactor all the occurences accordingly.

This change is part of an ongoing effort to eliminate global variables,
improve modularity and help libify the codebase.

Mentored-by: Christian Couder <christian.couder@gmail.com>
Mentored-by: Ghanshyam Thakkar <shyamthakkar001@gmail.com>
Signed-off-by: Ayush Chandekar <ayu.chandekar@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>