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I'm new to working in the shell and the usage of these commands seems arbitrary. Is there a reason one flag has a single dash and another might have a double dash?

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A single hyphen can be followed by multiple single-character flags. A double hyphen prefixes a single, multicharacter option.

Consider this example:

tar -czf

In this example, -czf specifies three single-character flags: c, z, and f.

Now consider another example:

tar --exclude

In this case, --exclude specifies a single, multicharacter option named exclude. The double hyphen disambiguates the command-line argument, ensuring that tar interprets it as exclude rather than a combination of e, x, c, l, u, d, and e.

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    @kylex, no, since there is no long option named just "c" and the -- means a long option, not a single character option follows. – psusi May 10 '12 at 14:37
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    Sometimes even long commands can be single-dashed. For example 'cdrecord' uses all single-dashed commands (-eject -dao ...). It all depends on the program, but most(!) of them use - for single and -- for multiple-character (long) commands – mulaz May 10 '12 at 14:42
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    @mulaz, yes, cdrecord does quite a few goofy things. – psusi May 10 '12 at 14:46
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    also bear in mind -- used on its own usually signifys the end of options. see here for more info: unix.stackexchange.com/questions/11376/… – Sirex May 10 '12 at 19:51
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    @killjoy, because whether through ignorance or choice, the authors of those programs did not follow the convention of course. Just like cdrecord mentioned years ago in the above comments. – psusi Apr 2 '18 at 15:25
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It all depends on the program. Usually "-" is used for 'short' options (one-letter, -h), and "--" is used for "long"(er) options (--help).

Short options can usually be combined (so "-h -a" is same as "-ha")

In Unix-like systems, the ASCII hyphen–minus is commonly used to specify options. The character is usually followed by one or more letters. An argument that is a single hyphen–minus by itself without any letters usually specifies that a program should handle data coming from the standard input or send data to the standard output. Two hyphen–minus characters ( -- ) are used on some programs to specify "long options" where more descriptive option names are used. This is a common feature of GNU software.

source

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    So why is it java -version and ant -version, then ? – killjoy Mar 30 '18 at 14:48
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It's really a convention. However, it can aid parsers to know more efficiently about options passed to the program. Besides, there are neat utilities that can help parsing these commands, such as getopt(3) or the non-standard getopt_long(3) to help parse the arguments of a program.

It is nice, for we can have multiple short options combined, as other answers say, like tar -xzf myfile.tar.gz.

If there was a "lisa" argument for ls, there would probably have a different meaning to type ls -lisa than ls --lisa. The former are the l, i, s, and a parameters, not the word.

In fact, you could write ls -l -i -s -a, meaning exactly the same as ls -lisa, but that would depend on the program.

There are also programs that don't obey this convention. Most notably for my sight, dd and gcc.

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short options with single dash vs long options with double dash

short options can be combined into a single argument; 

for example: ls -lrt #instead of ls -l -r -t

If we allow long options with single dash, it causes ambiguity. To resolve this we use double dash for long options.

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