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In the run/debug configuration that will be used for launching the app, click the Logs tab. The Edit Log Files Aliases table displays the list of log files. Select Save console output to file Specify the path to the file.
Run tool window The Run tool window displays output generated by your application. If you are running multiple applications, each one is displayed in a tab named after the run/debug configuration applied. If you re-run an application, the new output overwrites the contents of the tab.
Preferences/Settings -> Editor -> General -> Console, check the box next to Override console cycle buffer size, set to a larger number than 1024 KB.
Couldn't get more votes to close the question so I have to answer it myself.
IDEA_HOME\bin\idea.properties
#-----------------------------------------------------------------------
# This option controls console cyclic buffer: keeps the console output size not higher than the specified buffer size (Kb). Older lines are deleted.
# In order to disable cycle buffer use idea.cycle.buffer.size=disabled
idea.cycle.buffer.size=1024
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