Wow... this was hard to understand...
You wan't a persistence system, for more info read: http://en.wikipedia.org/wiki/Persistence_%28computer_science%29
You will always need an in-memory list or array (obviously reading from disk all the time is way too expensive).
Short answer, yes it's possible to implement an incremental persistence system, for example using XML.
It won't be easy if you don't have experience with XML (reading and writing), you will need to use DOM, no SAX, good thing is that both Java and PHP have great support for it.
Anyway I'd recommend a relational database system, such as SQL...