Bootloader in same Flash as application?

Is it possible to have a separate bootloader and application in the same flash? The problem I see is hooking the interrupts from the low memory (the bootloader's to go into 0x0000)into the application which uses them.

Do I have to compile these applications into
one application, to get the interrupts
hooked in? I'd rather these programs
not be dependent on each other.

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