Improved `file` source checkpointing

The Vector file source included an option called start_at_beginning that would determine where Vector would begin reading a file based on a variety of conditions. As you can see, these conditions were quite confusing. To resolve this, PR 6178 deprecated the start_at_beginning option and replaced it with new ignore_checkpoints and read_from options. Migrating is easy:

 [sources.file]
 type = "file"
-start_at_beginning = true
+ignore_checkpoints = false # default
+read_from = "beginning" # default

Adjust as necessary. The above values are the defaults and are not required to be specified.