Breakpoints not working in 2016.2.4

Seems to be similar problem as is similar earlier versions, no checkmark on the the red circle when debugging the project, doesn't stop on the breakpoints anywhere. After debug is started console does not show the usual " Listening for transport dt_socket at address: 53821" and "Listening for transport dt_socket at address: 53821
Connected to the target VM, address: '<hidden-personal-data>:53821', transport: 'socket'" it just runs the application.

Interestingly this does not happen on newly created skelton projects. Just on my developemnt project. Zip file attached

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*Imported from [IDEA-161638](https://youtrack.jetbrains.com/issue/IDEA-161638) · Type: Bug · Votes: 0*
*Comments, attachments, dates and reporter are not part of the export — follow the link above for the full history.*

Start by reproducing the breakpoint behavior with the attached development project and compare it with a newly created skeleton project. Check the debugger startup output for the missing transport messages; done means breakpoints are marked and execution stops in the development project.

Written by the indexing model from the issue text.