t/t3NNN: allow local submodules

To prepare for the default value of `protocol.file.allow` to change to
"user", ensure tests that rely on local submodules can initialize them
over the file protocol.

Tests that only need to interact with submodules in a limited capacity
have individual Git commands annotated with the appropriate
configuration via `-c`. Tests that interact with submodules a handful of
times use `test_config_global` instead. Test scripts that rely on
submodules throughout use a `git config --global` during a setup test
towards the beginning of the script.

Signed-off-by: Taylor Blau <me@ttaylorr.com>

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