Where can I find the eclipse store preferences in the file system

Eclipse stores the preferences in the workspace of your application in the.metadata/.plugins/org.eclipse.core.runtime/.settings/ directory in the <nodePath>.prefs file

For example, for CDT build environment variables stored in here:

.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.cdt.core.pref

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Java processes and streams and avoiding blocks

One of the best resource on managing the streams in Java
https://wiki.sei.cmu.edu/confluence/display/java/FIO07-J.+Do+not+let+external+processes+block+on+IO+buffers