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As far as I can tell <workspace>/.metadata/.plugins/org/eclipse.jdt.core/savedIndexNames.txt is the only place where the absolute pathname of the workspace is stored in metadata. Using relative pathnames (i.e. just the simple filenames) would be sufficient because all the files are in the same directory. This would reduce the disk space required to store the information; it would reduce the IO required save/restore the data; and it might reduce the in memory size of data structures relating to the index.
Kent can you please comment ?
This was done as part of the changes to bug 138309
Verified for 3.3M5 using I20070205-0009. The index version however has a full path.: INDEX VERSION 1.120+D:\eclipse\workspaces\testM5\.metadata\.plugins\org.eclipse.jdt.core