Yes it can. Signed applets have access to the FileSystem.
Personally, I'd never use either - unless I was explicitly told to by a customer. But Flash is not backed by as rich a programming language as Applets are so, though you can do a lot with Flash, you can do a lot more with Applets.
You do IO with applets the same way you do IO in applications. You just have to prove your applet is not malicious. See Advanced Programming for the Java 2 Platform: Chapter 10: Signed Applets for an example.
Applet in it's behaviour is like ActiveX control on web page for Java. You can do much more with Applet's than Flash. Altough if you are interested only in graphics with Macromedia you will do it 1000s times faster. Applets are for programmers, flash is for web designers.
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