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Ensure that we include conflicts when calling `git_index_read_index`,
which will remove conflicts in the index that do not exist in the new
target, and will add conflicts from the new target.
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Use legitimate (existing) object IDs in tests so that we have the
ability to turn on strict object validation when running tests.
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It's not always obvious the mapping between stage level and
conflict-ness. More importantly, this can lead otherwise sane
people to write constructs like `if (!git_index_entry_stage(entry))`,
which (while technically correct) is unreadable.
Provide a nice method to help avoid such messy thinking.
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When adding a conflict for some path, remove the staged entry.
Otherwise, an illegal index (with both stage 0 and high-stage
entries) would result.
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This was not converted when we converted the rest, so do it now.
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