fix(config): avoid config duplications

[becm]

Avoid duplication of entries already present in included files:

• consistent include of files in Git config queries with scope limit
• fix inconsistencies in setup state detection
• avoid blind updates without checks, as Git will ignore existing entries in includes

Improves consistency regarding include behavior with cached Git config and

Fixes #2342
Fixes #1696
Fixes #1337

[derrickstolee]

@becm Thanks for identifying this key piece that connects to several issues. Could you add a test to demonstrate the behavior change to prevent regressions in the future?

[becm]

@derrickstolee sadly only the 1st step, since:

• the assignment seems to be unconditional
• I did not even manage to get all instances where the --list request is issued.

[becm]

@derrickstolee since the --include stuff is dependent on partnered Git version and file setup, I'd have no idea how to attempt a proper test (existing examples just operate on unrelated mock data).

Will try to implement a test for (abstract) config data with the (hopefully) resolved corner case of configure.