While trying to troubleshoot copying from the root I ended up testing using the --include flag. I was previously adding my filters in a manifest.txt file and passing it in with --include-from.
Running the copy command with --dry-run -P -vv, I can see that the filter is actually being applied. I only just learnt about the -vv flag as I came here to ask for help.
The output from -vv and your comment has now revealed my real problem which is:
rclone is traversing sub folders of other folder within my storage.
The other folders could contain thousands of files which causes the copy command to run for a very long time.
How do I prevent this behavior and copy only the files/folder in the manifest.txt without traversing other directories?
2022/06/06 18:16:38 DEBUG : rclone: Version "v1.58.1" starting with parameters ["C:\\Tools\\rclone.exe" "copy" "remote:" "--include-from=C:\\Users\\user\\manifest.txt" "C:\\Dest" "--dry-run" "-P" "-vv"]
2022/06/06 18:16:38 DEBUG : Creating backend with remote "remote:"
2022/06/06 18:16:38 DEBUG : Using config file from "C:\\Users\\user\\AppData\\Roaming\\rclone\\rclone.conf"
2022/06/06 18:16:38 DEBUG : found headers:
2022/06/06 18:16:43 DEBUG : Creating backend with remote "C:\\Dest"
2022/06/06 18:16:43 DEBUG : fs cache: renaming cache item "C:\\Dest" to be canonical "//?/C:/Dest"
2022-06-06 18:16:44 NOTICE: Readme.md: Skipped copy as --dry-run is set (size 1)
2022-06-06 18:16:47 NOTICE: Photos/Coast.jpg: Skipped copy as --dry-run is set (size 800.553Ki)
2022-06-06 18:16:47 NOTICE: Photos/Nut.jpg: Skipped copy as --dry-run is set (size 932.643Ki)
2022-06-06 18:16:47 NOTICE: Photos/Hummingbird.jpg: Skipped copy as --dry-run is set (size 571.503Ki)
2022-06-06 18:16:47 DEBUG : Documents/About.odt: Excluded
2022-06-06 18:16:47 DEBUG : Documents/About.txt: Excluded
2022-06-06 18:16:52 DEBUG : Local file system at //?/C:/Dest: Waiting for checks to finish
2022-06-06 18:16:52 DEBUG : Local file system at //?/C:/Dest: Waiting for transfers to finish
Transferred: 2.251 MiB / 2.251 MiB, 100%, 328.279 KiB/s, ETA 0s
Transferred: 4 / 4, 100%
Elapsed time: 13.5s
2022/06/06 18:16:52 NOTICE:
Transferred: 2.251 MiB / 2.251 MiB, 100%, 328.279 KiB/s, ETA 0s
Transferred: 4 / 4, 100%
Elapsed time: 13.5s
Notice that the contents of Documents/ is read how do I avoid this because I'm only interested in Readme.md, Photos and whatever subfolders and files it may have?