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I have currently overseeing a system that has been passed to me, that the version control was done in this fashion:

Everytime the developer (just one) wanted to create a snapshot, he would copy the entire folder to a directory and give it a number. So currently I hold folders ranging from 1 to 50, and I would like to start using svn for this.

Besides from creating a new trunk from the last version, I would like to create a history from that versions. I tried copying versino 1, commiting, removing it, pasting v2 in place, commiting changes, it did work well, except for one problem (files deletes did not translate to svn deletes).

How would you automate this task?

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What you have described is what you will need to do. You can automate it (copying items is trivial to script). To capture the changes (adds, deletes, etc.) you can use svn_load_dirs.pl to handle detecting, performing & committing them.

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I don't know if you're on Windows or not, but TortoiseSVN, when you commit, lists the deleted files and allows checking them for SVN deletion.

Otherwise, you can have a look at the following question: How to remove all deleted files from repository?

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