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FP- yeah, not good for uploading alongside FTP. It caused me problems with "invisible files and folders" on the server - the advice from my tech and M$ is that you shouldn't be doing both in tandem.
Anyway, I guess the best answer depends on what is in each folder and how many folders you have.
If there are not many folders outside the ones you dont want to publish...use CTRL + click on the folders you want and right click to publish.
If there are a ton of other folders and that would take too long, you can select the log files in each folder and set them to "don't publish"
As for directly tagging folders not to be published....I ain't seen that option :(
Otherwise, IE aint bad at copying....just go to FILE > (check the open as web folder box) and type in your address
drag and drop what you want to put on the server.
They are workarounds if you can't find what you want :)
I also remember playing with another addin which pre-published your files to a temp folder without the FP extension folders so you could then FTP a clean version to your host. For the life of me I cannot remember the name other than it was a clever play on "Frontpage". I will go hunting, but in the meantime perhaps this will jog someone else's memory.
I think I need to clarify my situation a bit. The problem files are already on the server and FP keeps asking whether I want to delete each one of them.
For example, my web server at one host generates daily log reports and places them in a folder within my web. Every day a new set of files are entered here. When I publish with FP it goes thru each file in that log report directory and asks whether I want to keep each file. There is no Yes to All option...I have to click Yes for each one.
What I was looking for was some sort of way to stop FP from checking certain directories/files on the server when publishing. Maybe I'll have to switch to FTP only for this site.
I still remember that KISSfp software...It's starting to look better all the time ;)