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Ignore tree indices when deciding if things are in-sync if the user provides order-trees to acmd diff-root

Alaettin Serhan Mete requested to merge amete/athena:master-diff-root-update-2 into master

This fixes ATEAM-546. When we compare files w/ shuffled tree indices we shouldn't compare tree indices to decide if things are in-sync or not (since indices are obviously different). This essentially only changes the error messages and not the result of the test, which was anyhow correct.

I also updated the message to:

old_index.new_index.branch/variable_name old_value -> new_value => diff= [diff%]

to improve it.

BTW if the user doesn't provide --order-trees to acmd diff-root they won't notice anything.

cc: @jchapman

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