Slow down there buddy! You probably already have it...
Stop thinking about ebooks! You are limiting your possibilities by a lot.
Think DOCUMENT MANAGEMENT! Any program that can do this will do what you need. I work for a huge insurance company that has operations in all 50 states and many other countries. Because of legal mumbo jumbo we have to store many different copies of the same (almost the same) document in a manner that we can look it up easily. Sometimes they are in closed formats, editable formats, graphics, text only, draft, approved by legal, new editions, saved in English, German, French. Legal for New York, Legal for Texas, Legal in Michigan...you get the idea. It presents the same problem that we all have with our ebooks in their many formats.
Any basic database that allows you to make fundamental changes to field names (so you can name them intelligently - author, publish date, etc...) as well as link to a document will do the job better than 90% of what has been mentioned.
The database becomes your directory!
You can link one book to as many copies (formats) as you want, even if they are in completly different areas. The ebooks don't even have to be well organized - although I recommend it - because their location is no longer important. Just open the database, click on the title, then go to the link for what you need.
If you have access to any databse right now just look at what it does. You might see Name, Company, Address, Job title, photo - but if the field names can be edited it really says Title, Author, Genre, Publish Date and link to ebook.
You probably have what you need right now. Even better - you already know how to use it.
Good Luck!
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