Fix several places where files in .git/annex/ were written with modes that did...

Fix several places where files in .git/annex/ were written with modes that did not take the core.sharedRepository config into account.

git grep writeFile finds some more that might also be problems, but
for now I've concentrated on .git/annex/ log files. There are certianly
cases where writeFile is not a problem too.

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