How to sync two folders with command line tools?

This puts folder A into folder B:

rsync -avu --delete "/home/user/A" "/home/user/B"  

If you want the contents of folders A and B to be the same, put /home/user/A/ (with the slash) as the source. This takes not the folder A but all of it's content and puts it into folder B. Like this:

rsync -avu --delete "/home/user/A/" "/home/user/B"

• -a Do the sync preserving all filesystem attributes
• -v run verbosely
• -u only copy files with a newer modification time (or size difference if the times are equal)
• --delete delete the files in target folder that do not exist in the source

Manpage: https://download.samba.org/pub/rsync/rsync.html

You could unison tool developed by Benjamin Pierce at U Penn.

Let us assume you have two directories,

/home/user/Documents/dirA/ and /home/user/Documents/dirB/

To synchronize these two, you may use:

~$unison -ui text /home/user/Documents/dirA/ /home/user/Documents/dirB/

In output, unison will display each and every directory and file that is different in the two directories you have asked to sync. It will recommend to additively synchronize (replicate missing file in both locations) on the initial run, then create and maintain a synchronization tree on your machine, and on subsequent runs it will implement true synchronization (i.e., if you delete a file from .../dirA, it will get deleted from .../dirB as well. You can also compare each and every change and optionally choose to forward or reverse synchronize between the two directories.

Optionally, to launch graphical interface, simply remove the -ui text option from your command, although I find the cli simpler and faster to use.

More on this: Unison tutorial at Unison user documentation.

The answer from TuxForLife is pretty good, but I strongly suggest you use -c when syncing locally. You can argue that it's not worth the time/network penalty to do it for remote syncs, but it is totally worth it for local files because the speed is so great.

-c, --checksum
       This forces the sender to checksum every regular file using a 128-bit  MD4
       checksum.   It  does this during the initial file-system scan as it builds
       the list of all available files. The receiver then checksums  its  version
       of  each  file  (if  it exists and it has the same size as its sender-side
       counterpart) in order to decide which files need to be updated: files with
       either  a  changed  size  or a changed checksum are selected for transfer.
       Since this whole-file checksumming of all files on both sides of the  con-
       nection  occurs  in  addition to the automatic checksum verifications that
       occur during a file's transfer, this option can be quite slow.

       Note that rsync always verifies that each transferred file  was  correctly
       reconstructed  on  the receiving side by checking its whole-file checksum,
       but that automatic after-the-transfer verification has nothing to do  with
       this  option's  before-the-transfer  "Does  this file need to be updated?"
       check.

This shows how having the same size and time stamps can fail you.

The setup

$ cd /tmp

$ mkdir -p {A,b}/1/2/{3,4}

$ echo "\___________from A" | \
      tee A/1/2/x  | tee A/1/2/3/y  | tee A/1/2/4/z  | \
  tr A b | \
      tee b/1/2/x  | tee b/1/2/3/y  | tee b/1/2/4/z  | \
      tee b/1/2/x0 | tee b/1/2/3/y0 >     b/1/2/4/z0

$ find A b -type f | xargs -I% sh -c "echo %; cat %;"
A/1/2/3/y
\___________from A
A/1/2/4/z
\___________from A
A/1/2/x
\___________from A
b/1/2/3/y
\___________from b
b/1/2/3/y0
\___________from b
b/1/2/4/z
\___________from b
b/1/2/4/z0
\___________from b
b/1/2/x
\___________from b
b/1/2/x0
\___________from b

The rsync that copies nothing because the files all have the same size and timestamp

$ rsync -avu A/ b
building file list ... done

sent 138 bytes  received 20 bytes  316.00 bytes/sec
total size is 57  speedup is 0.36

$ find A b -type f | xargs -I% sh -c "echo %; cat %;"
A/1/2/3/y
\___________from A
A/1/2/4/z
\___________from A
A/1/2/x
\___________from A
b/1/2/3/y
\___________from b
b/1/2/3/y0
\___________from b
b/1/2/4/z
\___________from b
b/1/2/4/z0
\___________from b
b/1/2/x
\___________from b
b/1/2/x0
\___________from b    

The rsync that works correctly because it compares checksums

$ rsync -cavu A/ b
building file list ... done
1/2/x
1/2/3/y
1/2/4/z

sent 381 bytes  received 86 bytes  934.00 bytes/sec
total size is 57  speedup is 0.12

$ find A b -type f | xargs -I% sh -c "echo %; cat %;"
A/1/2/3/y
\___________from A
A/1/2/4/z
\___________from A
A/1/2/x
\___________from A
b/1/2/3/y
\___________from A
b/1/2/3/y0
\___________from b
b/1/2/4/z
\___________from A
b/1/2/4/z0
\___________from b
b/1/2/x
\___________from A
b/1/2/x0
\___________from b