Thanks, r3sistance. That is indeed unusual. :-) I just executed the command on my system and dir1 and file1 were both copied into dir0.

If I deleted the destination folder, dir0, then it works.
Meaning content of dir were copied to dir0.

BUT....
If I create (mkdir) dir0 before cp command, only directories were copied!
What did I missed?

In case it has not already been asked of you, which shell (and version) are you using?

echo $0 will give you the shell name.

Your package manager will give you the version e.g. dpkg -l bash

On my system, where the non-hidden directory and file are copied across, but not the hidden file (as I would expect) I'm using Bash 4.3.

If indeed your original post examples are correct, the problem is not with the cp operation:

All of the red commands should produce the same result.

Filesystem corruption maybe? Or do you have some weird aliases, or symlink or hardlink on those?

What do the following show:

And a little more context: Is this on a local machine or some remote machine? What distro, version, etc.? And as others have asked, what shell?

Not on my system they don't (Mint 18.1, Bash 4.3).

Given the directory contents generated by the OP's commands, the output from the various ls commands in question on my system mimics the OP's. It's just the results of the cp that differ between this system and theirs.

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I stand corrected!

OK, I see what is happening but will completely form my next thought before posting...

A thousand apologies.
I took a break... and came back and check my work.
My eyes were playing games on me.
cp does work.
Please ignore my posts about missing files when doing cp.
All your generous posts were correct, except mine!
Sorry again.

No problem! The most important thing is that your query was solved and that you understand what was happening.

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This almost looks like a clever juxtaposition of behaviors forming a kind of edge case, but I guess someone has to trip over it eventually.

The confusion results because of the difference between cp -a dir and cp -a dir/*, and because of two different destinations cases: dir0 exists, and dir0 does not exist. Finally, a subtle default behavior of the ls command conspires to further obscure the final result...

First, the behavior of cp:

* When you use cp -a dir you are copying the directory itself, and therefore everything in it, to some destination.
* When you use cp -a dir/* you are copying non-hidden files and directories within dir/ only, hidden files are not copied!

And

* When dir0 exists, the intended behavior of cp is to copy the source, dir, into the destination, dir0
* When dir0 does not exist, cp copies the source directory to a new directory named dir0, not INTO dir0

Clearly this is the observed behavior and others have correctly explained it this way.

Finally, the behavior of ls:

* When ls -al lists the contents of dir0 it lists ., .. and dir/, correctly.
* When ls -al lists the contents of dir0/*, it lists the only non-hidden thing there, dir/, exactly as it should.

BUT - in this last case, when it lists the directory contents, and there is only one directory item, it does not print a heading clearly showing it to be a subdirectory. If you add a visible file in there or another directory, it will clearly add the subdirectory heading.

It is this last condition which is subtle and which we do not often see which allows us to become confused!

As such, I have to think this was a cleverly contrived example. If not, it ought to be!

Fanoflg, where did you find this?

*** I see it is now solved, good luck!

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cp -a will work on all files, including hidden, -a is archive. If you want all the folder "~/dir" with ALL files inside of ~/dir0 -- Try with an ending / and -f, a wildcard isn't necessary here. Are all the files/folders being used with a privileged user / has correct permissions?

cp -af ~/dir/ ~/dir0/

Also consider running the command in verbose(-v) or interactive(-i) for answers.

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Thank you for your analysis.
I did not find it anywhere.
I was learning about cp and decide to make up directories and files for testing.

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Well, it was certainly educational!

It really does create a clever trap for those not paying attention (like me, and should have been).

Glad you found the answer, and thanks to all who helped!

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