By a popular request Override console cycle buffer size setting was added to the UI 9/14/16:
Original answer for older versions:
Edit your IDEA_HOMEinidea.properties
file, and increase this setting:
#-----------------------------------------------------------------------
# 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
then restart IntelliJ.
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