An internal error occurred during: "Initializing Java Tooling"

Do not delete all the full .metadata

• Backup .metadata
• delete only .metadata/.plugins/org.eclipse.core.resources/.project
• restart eclipse

Observation : the projects folders are created

Further - if you are using svn/git/hg have code repository links it would be destroyed, so to reinstate

• close eclipse
• copy relevant projects from backup to merge with current projects in .metadata/.plugins/org.eclipse.core.resources/.project
• restart eclipse

Downfall - sporadic fail error may occur (sync or something) - harmless