A typical application like ERP, I always need keep look and feel of prototypes consistency every-time I release the prototype while requirements change all the time. Useful tools have these characteristics:

A. Must have
    1. Create Master Page/Page template with editable region: Keep page outline consistency.
    2. Create UI Snippet, drag drop snippet to interface.
    3. Update original snippet will update this snippet everywhere in current project.
    4. Link support
    5. Show a map of linked pages/site map
    6. Export to pictures
    7. Export to html

B. Nice to have:
    1. Note and document
    2. Tracking change
    3. Support collaboration

What tool is suitable for this kind of application?

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Check out Axure. I've been evaluating it for a few projects that I've been scoping out and it is working pretty well. It's a little pricey, but well built. The only "Must have" that I think it will be weak on is #1. Although, I can think of a few ways to make it do what you want. It also covers several of your "Nice to have"s. Definitely worth a look.

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Although I don't use Indesign, I think EightShapes has a great workflow set up for reusable components for all your deliverable needs including prototyping. If nothing else it is some good inspiration.

My personal favorite is Adobe Fireworks. You can have a master page, share layers between pages, create graphics that when updated are updated everywhere, create buttons that are like graphics but you can change the text individually, and also it has 'auto shapes'. A good example of 'auto shape' power is the Placeholder auto shape by John Dunning. It will create a image placeholder that updates it's label when you resize it.

You can also create a clickable prototype for the browser or an interactive pdf with ease.

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