Eclipse modify classpath on its own

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I have a quite annoying issue with Eclipse and the .classpath file. I usually used variable in my build path in order to be able to change of version easily. The issue with Eclipse its that the software break the variables set and put the build path in lib mode instead of var.

for example from a var like that :

<classpathentry kind="var" path="NIAGARA_HOME/modules/platform.jar"/>

it destroy the kind and put it like that :

<classpathentry kind="lib" path="C:/Niagara/Niagara-3.7.106/modules/platform.jar"/>

and same thing for the JRE set :

<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>

to :

<classpathentry kind="lib" ----- etc.

i didn't put the whole code of the JRE since it call directly each .jar file used in my project.

How is it possible to fix it ? First I think it come from the issue when Eclipse is starting and doesn't find the variables set and automatically destroy all relation of var into lib.

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