Updating the links to migrated Evolving java based APIs part 1, part 2
and part 3.

API execution environments as described in the old BREEs link are not
available anymore to be installed, for example in
https://download.eclipse.org/eclipse/updates/4.29/ Therefore replace the
link to the BREE wiki with a semantic description.

Link to Ganymede removed as 3.4 is old and not worth mentioning that
this feature is available since 3.4.

Link to JDT wiki replaced with link to JDT github project

Link to API wiki replace with link to official API tools help in the
Eclipse help.