For Stratix® IV GX, Stratix IV GT, Stratix IV E, Arria® II GX, and HardCopy® III devices the BSDL file pre-configuration and post-configuration generation is now generated and customized in the Quartus® II software.
To generate a BSDL File in the Quartus II software:
1) On the Assignments menu, click Settings.
2) In the Category list, select Board-Level under EDA Tool Settings.
3) In the Board-level boundary scan box, select BSDL from the Format list.
4) Type or browse to the location you want to use as the output directory for the BSDL File. The default location is <project directory>/board/bsd.
5) Select either Pre-configuration BSDL file or Post-configuration BSDL file.
6) To generate the BSDL File, compile the design.
For more information and example on how to use a tcl script to generate BSDL files in the Quartus II software, refer to Altera BSDL Support.