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Is there any diff tool for Lotus Notes which allows to compare scripts, design elements and documents?
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This is what I do. I run a design synopsis of the database using the Notes Designer. Dump the file to a text file. You can actually split the synopsis out to different objects like Agents, Forms, Views, etc. Then you can run UNIX/Linux/Mac Unix commands to compare the elements. By doing this operation you find out what code is active, and have a complete documented source code. You do a lot of csplit and a few sed commands.
I see this is an old question, and most of the other answers are a little outdated now, so I thought I would add some hopefully valuable information for those who should stumble upon this now.
In Domino Designer, open either the Navigator or Package Explorer (Window menu -> Show Eclipse Views). Here you can expand databases/templates to see the design elements they contain. Select two or three elements (CTRL-click). They can be in different databases or the same database. Right click on one of the elements and select Compare with -> Each other.
You can also compare two databases element by element by selecting two databases/templates, right-clicking and selecting Compare with -> Each other. You will then get the differences between the two databases listed. You will be able to see which elements differ between the two databases, and which elements exist in one database but not the other. By double-clicking on a differing element, you will open a diff tool which lets you see differences line by line, and you can easily copy changes from left to right or right to left.