SSH command with file redirect not working

I'm going to accept derobert's answer because it gave me information I needed. I still had issues, which I think might of been my awk command, which I replaced with an alternative approach. The following is what I did to ensure my authorized_keys file on the remote server had only unique entries:

ssh [email protected] "sort /root/.ssh/authorized_keys | uniq > /root/.ssh/temp"
ssh [email protected] "mv -f /root/.ssh/temp /root/.ssh/authorized_keys"

Here's everything you need to know about quoting something to protect it from shell expansion and word-splitting:

1. Enclose everything other than apostrophes between apostrophes. For example, do not becomes 'do not'.
2. Use backslashes to escape apostrophes, i.e. ' becomes \'.
3. Break your string up into apostrophes and other characters, apply the preceding 2 rules, then concatenate the results. For example, don't becomes 'don'\''t'.

With these general rules, the command in your question can be properly quoted as follows:

ssh [email protected] 'awk '\''!seen[$0]++'\'' /root/.ssh/authorized_keys > /root/.ssh/authorized_keystemp'

There are more readable ways to quote the same string, but this approach is generally applicable and easy to visually verify as correct.

I find myself doing this often enough that I wrote a shell function/script to do it for me, and I use it all the time. Here it is:

#!/bin/sh -

# shellquote foo => foo
# shellquote foo&bar => 'foo&bar'
# shellquote foo'bar => 'foo'\''bar'
shellquote() {
  local input="$1"
  local output=""
  local backslash='\'
  local apostrophe="'"
  if [ -z "${input}" ]; then
    # Empty string => pair of apostrophes
    output="''"
  fi
  while [ -n "${input}" ]; do
    case "${input}" in
    "'"*)
      # Escape the apostrophe.
      output="${output}${backslash}${apostrophe}"
      input="${input#${apostrophe}}"
      ;;
    *"'"*)
      # Quote everything before the first apostrophe, and then escape
      # the apostrophe.
      output="${output}${apostrophe}${input%%${apostrophe}*}${apostrophe}${backslash}${apostrophe}"
      input="${input#*${apostrophe}}"
      ;;
    *[!+,./0-9:=@A-Z_a-z-]*)
      # There are no apostrophes, but at least one character needs quoting.
      # So quote the entire word.
      output="${output}${apostrophe}${input}${apostrophe}"
      input=""
      ;;
    *)
      # Nothing needs quoting. Output everything literally.
      output="${output}${input}"
      input=""
    esac
  done
  printf '%s' "${output}"
}

main() {
  local sep=''
  for arg; do
    printf '%s' "${sep}"
    shellquote "${arg}"
    sep=' '
  done
}

main "$@"