why do we need to re-organize the code of open source library?

I am new to TLC (TrueLicense Code) project and I have donloaded from here http://java.net/projects/truelicense/. When I added this project to Netbeans IDE it thrown exeception "badly formed project". I organized source or class files according to directory hierarchy that maps to package name.

e.g. A downloaded Class LicenseContent.java belongs to the package de.schlichtherle.license therefore source code must be organized according to this hierarchy. JVM only accepts when we map folders according to packages.

When I downloaded I had three folders -

1. truelicense-core
2. truelicense-swing
3. truelicense-xml

and they are badly formed because classes into truelicense-core folder imports many classes from truelicense-xml and they also have there package hierarchy. So we have to rearranged them to use in our projects.

1. com >> nexes >> wizard
2. de >> schlichtherle >> license/ swing/utils/xml
3. resources >> contains all properties file.

I am very curious to know why these code is organized differently then what jvm would accept?