Glob files and sort by filemtime and into months

Since your end-goal is to group the filenames by month, you need a loop to show you only the entries from the $files array that match a particular month:

$months = array(
    '2018-07',
    '2018-06',
    '2018-05',
    '2018-04'
);

foreach ($months as $month) {
    // just some example markup
    echo '<p>' . $month . '</p>';

    echo '<ul>';
    foreach ($files as $path => $timestamp) {
        if (date('Y-m', $timestamp) == $month) {
            echo '<li>' . $path . '</li>';
        }
    }
    echo '</ul>';
}

If you already know that you're not going to use your $files array for anything else, another option might be to simply group the files while processing the glob results:

foreach (glob("*.php") as $path) {
    $timestamp = filemtime($path);

    $files[date('Y-m', $timestamp)][$path] = $timestamp;
}

Since it's now a nested array, you can't simply arsort() the whole thing. But you can delay that until you want to loop over the file list to generate the desired HTML output:

// first sort the whole thing by keys (year + month), so that the months are sorted:
krsort($files);

foreach ($files as $month => $paths) {
    // now sort the paths by their timestamps
    arsort($paths);

    // and output whatever markup you want
    echo '<p>' . $month . '</p>';

    echo '<ul>';
    foreach ($paths as $path => $timestamp) {
        echo '<li>' . $path . '</li>';
    }
    echo '</ul>';
}

EDIT AFTER THE UPDATED QUESTION

You seem to be misunderstanding a basic concept of defining variables in loops.

You have two separate loops in your code: one that processes the result of glob() and one that turns the result of that processing into markup for your jQuery accordion.

By defining $monthname in the first loop, it will maintain its last value when processing the glob() result is finished.

You want to use $monthname in the second loop, but you're not setting it there. Therefore, it will always be the same value: the last value it was when processing the glob() result. Instead, you should define $monthname where you want to use it.

Sidenote: I used date('Y-m') in my answer as an example, since I didn't know what you were going to display. If you always want to display the date as date('F'), you can simply use that for the array key instead. Then there's no need to keep track of a separate $monthname variable and you can simply output the $month value in the second loop. However, this might not be what you want, if you have files in there that have been modified in the same month but in different years.

As for the specific warnings you're seeing, they are caused by the fact that you're storing each file into the $files array twice now:

foreach (glob("*.php") as $path) {
    if($path == 'index.php') {
    continue;
    }  // removes all files names index.php

/**** HERE: ****/
    $files[$path] = filemtime($path);

    $timestamp = filemtime ($path);
    // needed to define $timestamp

/**** AND HERE: ****/
    $files[date('Y-m', $timestamp)][$path] = $timestamp;

    $monthname = (date('F', $timestamp));
    // display month full name instead of month numeral
}

This means that the $files array looks something like this:

Array
(
    [/var/www/file.php] => 1529239095
    [2018-06] => Array
        (
            [/var/www/file.php] => 1529239095
        )

)

Because you still have that first assignment in there, you now occasionally try to sort (which you copy/pasted incorrectly, it should be an arsort() instead of krsort()) a timestamp (integer) instead of an array of path => timestamp entries. You should remove that first assignment.

This seems to be covered as an issue in this bug report on php.net: https://bugs.php.net/bug.php?id=33047

The last post on that thread is about it not being a bug, but an issue from how glob treats brackets, as part of the regular expression. I'm not sure I agree. It seems you can work around this, unless you cannot move up into the parent folder.

If you remove the first requirement of being in the inside [test] folder, you can get the file listing by using a syntax like below:

chdir('..');
$glob = glob("[[]test[]]/*");

Given these complications, I would recommend not using the glob function if you are running into issues on windows machines, and look at other file listing functions like readdir.

I agree that using rsync would be a better solution, but there is an easy way to skip a directory in bash:

for file in "$HOME/"*
do
    [[ $file = $HOME/Backup ]] && continue
    cp -r "$file" "$HOME/Backup/"
done