when you build/deploy a SSIS project a manifest file will be created and a copy of all the projects packages will be placed in the directory you specified, this is the /bin by default. The manifest is an executable that will install the SSIS packages when ran on the server.
If you are doing a filesystem install you really don't need to do this. The files placed in the /bin are exactly the same as those in your project folder. Under a file system package deployment you can simply copy your project pacjages to the directory you want to run them from on the server. This can be any directory, but if you want them to be displayed under the SSIS server in SSMS they need to be placed in a directory that is typically 'InstallPath'\90\DTS
you can make sub directories in here that will be displayed in SSMS.
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