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[news.eclipse.tools] Why does Eclipse track file state between invocations?

Initially we will use a non-Eclipse-supported SCM system.  This means our
developers will manage the files outside the Eclipse platform.  We
understand that files changed while the platform is running must be
"Refreshed from Local".

We expected that any files changed while the platform is NOT running would
be transparent to the Eclipse platform.  That is, after using our external
SCM, we expected that we could launch the Eclipse platform and it would
automatically pickup the changed files.  However, this is not the case: 
The Eclipse platform appears to remember the previous file state, so we
are forced to "Refresh from Local".

Question:  Why does the Eclipse platform track file state between
invocations?

Thanks.

-- Steve