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If you chain workflow commands together in Windows they can't be separated with ';' but rather rather '&&' is required as the separator.
Funnelback distorts this command if it has parameters (e.g. trying to kill and then scope the index). If you need to specify multiple commands, group them in a batch script. For example:
:: Author: Funnelback consultant :: Description: Script for post_index_command :: Version: 0.1 :: Last update: 5th August 2011 :: Kill specific pages from the index \bin\padre-fl.exe \data\<COLLECTION>\offline\idx\index \conf\<COLLECTION>\kill-exact.cfg \-exactmatch \-kill :: Scope the collection as normal \bin\padre-gs.exe \data\<COLLECTION>\offline\idx\index \conf\<COLLECTION>\gscopes.cfg 0 \-separate
If you want to make use of the $CURRENT_VIEW and $COLLECTION name variables from within your script you should pass them in as parameters. $SEARCH_HOME is the only variable that is set in the global environment and available for use from your scripts.
... post_index_command=\conf\$COLLECTION_NAME\scripts\post-index.bat ...