Linux – What’s the best way to merge two directories on the same filesystem in linux

I would use rsync as it means that if it is interrupted for any reason, then you can restart it easily with very little cost. And being rsync, it can even restart part way through a large file. As others mention, it can exclude files easily. The simplest way to preserve most things is to use the -a flag – ‘archive.’ So:

rsync -a source dest

Although UID/GID and symlinks are preserved by -a (see -lpgo), your question implies you might want a full copy of the filesystem information; and -a doesn't include hard-links, extended attributes, or ACLs (on Linux) or the above nor resource forks (on OS X.) Thus, for a robust copy of a filesystem, you'll need to include those flags:

rsync -aHAX source dest # Linux
rsync -aHE source dest  # OS X

The default cp will start again, though the -u flag will "copy only when the SOURCE file is newer than the destination file or when the destination file is missing". And the -a (archive) flag will be recursive, not recopy files if you have to restart and preserve permissions. So:

cp -au source dest

There is a max-size option:

--max-size=SIZE         don't transfer any file larger than SIZE

So:

# rsync -rv --max-size=1.5m root@tss01:/tmp/dm

Will send only files less than 1.5m.

Regarding sizes from man: The suffixes are as follows: "K" (or "KiB") is a kibibyte (1024), "M" (or "MiB") is a mebibyte (1024*1024), and "G" (or "GiB") is a gibibyte (1024*1024*1024). If you want the multiplier to be 1000 instead of 1024, use "KB", "MB", or "GB". (Note: lower-case is also accepted for all values.) Finally, if the suffix ends in either "+1" or "-1", the value will be offset by one byte in the indicated direction*