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TMS320F280049C: How the file subdir_rules.mk is auto-generated in CCS v12?

Part Number: TMS320F280049C
Other Parts Discussed in Thread: C2000WARE, SYSCONFIG

Open a project in a new computer using a new version CCS from v11.01 to v12.0. All the environment and include path, etc. are changed in project property accordingly. Rebuild the project and everything is fine except that it still includes some paths that exist in the old computer which cause some warnings. It's found that the problem is because the old paths still exist in subdir_rules.mk file in one of the folders in the project. Only one of the folders. All other folders in the project are fine.

I am wondering how the subdir_rules.mk is auto-generated. Why the include paths in other folders are updated to the path in the new computer, but only the path in that particular folder is not.