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I'm currently working on a php project with 3 other people. I need a free software which can help me document the changes/revisions on the database and on the application that were developing.

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Maybe you want to be a bit more specific. If you are working with other people, is the revision control system you're using not enough? – slhck Jun 25 '11 at 8:36
Could you not just use git? Or is there some special functionality that is required? – slotishtype Jun 25 '11 at 10:04
@slotishtype: I'll try using Git, thanks for the comment. – Ieyasu Sawada Jun 25 '11 at 12:30
up vote 4 down vote accepted

As slhck suggests, I would use a revision control system to record changes, whenever you check in a change you have an opportunity to type in a message stating the reason for the change.

For database structure changes I use a revision control system to manage a set of SQL DDL commands "create table ...; create index ..." which I edit whenever I make a change (even if I normally do so by "alter table" etc). This then preserves a history of changes to the database structure. I use end-of-line comments in the DDL to record the purpose of the fields.

If this is insufficient for you, you might consider editing your question to clarify what you need.

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