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Some commands, such as rsync, take in lists as an argument. Can these files contain unix comments like #?

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Unless the documentation for the command explicitly mentions that it can contain comments, assume that it cannot.

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Concur. Generally, the respective manpage of the command will detail whether you can add comments to a read file, and if so how it identifies a line as a comment. – Shadur Oct 13 '11 at 9:58

What I usually do in cases like this, is build an arguments array (which can take comments) and then pass those along to rsync, for instance.

    # Show me what you're doing
    # All HTML and resources
    *.html *.css *.js
    # All PHP source code
    # To the live server
rsync "${rsync_args[@]}";
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If I understand you correctly, you want to add comments about files in the file list. This is not possible, because when shell encounters the # character, it will ignore all remaining character on the command line. One way to achieve this is to use rsync with --files-from=filelist argument. The filelist file can contain comments.

On the other hand, if you want to embed # characters in the filename, then this will work. For example, with bash:

touch a#b 
touch 'a #b' 
touch "a #b"
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See e.g. the --include-from argument of rsync. – Ignacio Vazquez-Abrams Oct 13 '11 at 12:12

Ignacio Vazquez-Abrams answer is the safest, but if you really want to do it (as I do in some instances), a simple workaround can easily get at least part-way there by dealing with # comments which take up the entire line.

Things can get a bit gnarly if you want to handle comments which follow the real list data-lines, unless you are certain that your data-lines contain no embedded # chars.

You can use process substitution and a simple helper script.

Here are some examples. The grc before diff generates coloured output.
I've used bash functions, but you can, of course, save them to a script file.

# nocom handles comment-only lines (ie. no dat)
#       it ignores any # chars embedded in your data lines.
  nocom() { sed -e '/^[[:space:]]*#/d' "$1"; }

# NOCOM handles handles comments which occurr after your data   
#       as well as comment-only lines.  
#       Do not use NOCM unless you are CERTAIN that your data
#       lines contain no  # chars.
  NOCOM() { sed -n '/^[[:space:]]*#/d; s/^\([^#][^#]*[^[:space:]]\)[[:space:]]*#.*/\1/; p' "$1"; }

printf '# a bit of hokus-pokus
        # you see the coments here, 
        # but the calling program will not.
$HOME/bin/kadabra  # comment after data
$HOME/bin/sim# another comment after data
' >file

echo == nocom ==
cat <(nocom "file")
echo == NOCOM ==
cat <(NOCOM "file")
echo == diff ==
grc diff "file" <(NOCOM "file")

Here is the output:

== nocom ==
$HOME/bin/kadabra  # comment after data
$HOME/bin/sim# another comment after data
== NOCOM ==
== diff ==
< # a bit of hokus-pokus
<         # you see the coments here, 
<         # but the calling program won't.
< $HOME/bin/kadabra  # comment after data
< $HOME/bin/sim# another comment after data
> $HOME/bin/kadabra
> $HOME/bin/sim
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