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This can probably become the most difficult task of the whole system. Providing transparent storage to the API classes is necessary so that we can completely abstract the user interface from the API. Here is a list of tasks that will need to be done by the backend.
The Bug, User, Comment and Attachment will all need to store their data to disk.
This will probably be the most commonly used task for the backend.
If a Bug has several comments, it will want to display the comments in the correct order.
There are two types of searching that will need to be done, a: the "open bug 305061" type of searching, and then there will be the reporting which will look more like "show me the last 5 closed bugs".
For RDBMS, this is not going to be too hard, but one of the requirements is file system based storage. Additionally, ensuring that several RDBMS can be used will require thought.
Please, give me your comments if you have any...
A separate file could be created for each backend. Each of these files would contain the same functions, each designed to do the work with it's particular backend. For example, the file filesystem.php might contain the functions needed for filesystem storage, while adodb.php might contain the same functions, but designed for use with the php adodb library.