Capturing the same regular expression over multiple lines - regex

Question

I want to capture series of file names that are listed each in a new line, and I have figured out how to capture the file name in the first line, but I haven't figured out how to repeat it on the subsequent lines.
# Input
# data/raw/file1
# data/raw/file2
# Output
# data/interim/file1
# data/interim/file2
Current Attempt
The regular expression I currently have is
# Input\n(# (.*))
And my inner capture group properly captures data/raw/file1.
Desired Output
What I want is to grab all of the files in between # Input and # Output, so in this example, data/raw/file1 and data/raw/file2.

Answer 1

Go with \G magic:
(?:^#\s+Input|\G(?!\A))\R*(?!#\s+Output)#\s*(.*)|[\s\S]*
Live demo
Regex breakdown
(?: # Start of non-capturing group (a)
^#\s+Input # Match a line beginning with `# Input`
| # Or
\G(?!\A) # Continue from previous successful match point
) # End of NCG (a)
\R* # Match any kind of newline characters
(?!#\s+Output) # Which are not followed by such a line `# Output`
#\s*(.*) # Start matching a path line and capture path
| # If previous patterns didn't match....
[\s\S]* # Then match everything else up to end to not involve engine a lot
PHP code:
$re = '~(?:^#\s+Input|\G(?!\A))\R*(?!#\s+Output)#\s*(.*)|[\s\S]*~m';
$str = '# Input
# data/raw/file1
# data/raw/file2
# Output
# data/interim/file1
# data/interim/file2';
preg_match_all($re, $str, $matches, PREG_PATTERN_ORDER, 0);
// Print the entire match result
print_r(array_filter($matches[1]));
Output:
Array
(
[0] => data/raw/file1
[1] => data/raw/file2
)

Answer 2

Using the s modifier, preg_match, and preg_split you can get each result on its own.
preg_match('/# Input\n(# (?:.*?))# Output/s', '# Input
# data/raw/file1
# data/raw/file2
# Output
# data/interim/file1
# data/interim/file2', $match);
$matched = preg_split('/# /', $match[1], -1, PREG_SPLIT_NO_EMPTY);
print_r($matched);
Demo: https://3v4l.org/dAcRp
Regex demo: https://regex101.com/r/5tfJGM/1/