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c-tree Utilities : Command-line utilities : ctutil : -compact

-compact
Compacts data file and rebuilds indexes using internal file definitions.
Usage
file is the name of the c-tree file. The default file extension (that is ".dat" if not configured differently) must be omitted. Relative paths are resolved according to the c-tree server working directory.
if the purgedups options is specified, all records with a duplicated primary key are removed from the file.

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