I want to check in a directory and all the sub-directories into the clear case. Is there a specific command to achieve it? Currently I am going into each directory and manually checking in each file.
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I would recommend this question:
(with 'ct being 'cleartool' : type 'doskey ct=cleartool $*' on Windows to set that alias)
But if by "checkin" you mean:
I would recommend creating a dynamic view and clearfsimport your snapshot tree (with the new files) in the dynamic view.
See this question or this question.
:
did you used -recurse option in the clearfsimport command. Example: clearfsimport -recurse source_dir .
This should help. If you're using the Windows client, right-click on the parent folder, select Search, leave the file name field empty, click Search, select all the files in the result window (ctrl-A), right-click on them and select ClearCase -> Add to Source Control
If you are in windows you may try,