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For a deployed application to work properly, the database server and client applications must each be able to locate the files they need. The deployed files should be located relative to each other in the same fashion as your SQL Anywhere installation.
In practice, this means that on Windows, most files belong in a single directory. For example, on Windows both client and database server required files are installed in a single directory, which is the win32 subdirectory of the SQL Anywhere installation directory.
For a full description of the places where the software looks for files, see How SQL Anywhere locates files.
Linux/Unix/Mac OS X deployment issues
File naming conventions