For your question on installing upgrades to a Linux server, you do need to remove the read-only attributes for Adagio program files before installing upgrades or additional new applications. Unlike Windows, Linux really won't let an installation over-write files with a read-only attribute. The Adagio install would have to not install any files with a read-only attribute, and until this is changed, you would have to go through this procedure manually.
As for your Inventory Receipts vs. Order Entry question, it seems very reasonable that files with read-only attributes would cause problems in writing to those files.
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Softrak Tech Support