Deprecate unused methods in `FileNamingStrategy` and `FileHierarchy`

```java
edu.ie3.datamodel.io.naming.FileNamingStrategy#getIdCoordinateFilePath
edu.ie3.datamodel.io.naming.FileHierarchy#getBaseDirectory
edu.ie3.datamodel.io.naming.DefaultDirectoryHierarchy#getBaseDirectory
edu.ie3.datamodel.io.naming.FlatDirectoryHierarchy#getBaseDirectory
```