How to read and/or edit the new ".ise" Project Navigator project file
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In the "%Xilinx%\data\projnav" directory there is a script file named "iseEdit.tcl." This script was created to import and export ISE file content.

Usage:
xtclsh iseEdit.tcl [export|import] [client=<client_name>] [datafile=<datafile_name>] [<projectname.ise>]

Valid options are:
help : Displays this help message
export : Exports contents of the client registry section to a datafile
import : Imports contents from a data file to the client registry section
(Note: Either the -export or -import option must be specified, but not both)

client=<clientname> : Optionally specify the client to use. If not specified,
'ProjectNavigator' is used as the default client

datafile=<datafile_name> : Optionally specify the data file to use for export or import

<projectname.ise> : ISE Project file name to use for export only. This must be
specified for export but should not be specified for import

Examples:
xtclsh iseEdit.tcl export watchvhd.ise
xtclsh iseEdit.tcl import

xtclsh iseEdit.tcl export datafile=pndata.txt watchvhd.ise
xtclsh iseEdit.tcl export client=ProjectNavigator datafile=pndata.txt watchvhd.ise
xtclsh iseEdit.tcl import datafile=pndata.txt

xtclsh iseEdit.tcl import client=ProjectNavigator datafile=pndata.txt