To answer this question, the user needs to know the basics of file-based databases and their disadvantages.

File-based databases are systems that store data in individual files. Each file contains a unique set of data, and related files are linked together to create a database. Although file-based databases were once popular, they have several disadvantages that make them less desirable than modern database management systems (DBMSs).

Now, let's go through each option and explain why it is right or wrong:

A. Repetition of data: This option is correct. In file-based databases, each file contains its unique data, which means that the same data can appear in multiple files. This redundancy can lead to inconsistencies and data synchronization issues, which can be difficult to resolve.

B. Separation of data: This option is correct. Since file-based databases store data in individual files, related data can be spread over multiple files. This separation of data makes it challenging to retrieve data from multiple sources and can lead to issues with data integrity.

C. Incompatibility of files: This option is correct. Different file-based databases may use different file formats, making it difficult to share data between systems. This incompatibility can lead to issues with data migration and system interoperability.

D. Data dependence: This option is correct. The data in file-based databases are typically tightly coupled with the applications that use them. This dependence can make it challenging to modify or update the database without affecting the application, leading to issues with maintainability and scalability.

E. All of the above: This option is correct. All of the above options describe the disadvantages of file-based databases.

Therefore, the correct answer is: E. All of the above.