dune keeps no longer existing files from data_only_dirs in _build #2499
Description
I have an rule with a dep to a source_tree (let's say it's named spec). The alias generates a dune file based on the content of spec. It mostly does what I expect. Except when I run this alias after removing a file from spec. Because the content of spec in _build will still contain the file which was removed in the real spec. It seems to be because I marked the spec directory with data_only_dirs.
I created a small project to reproduce https://github.com/Khady/dune-data-only-dirs-cleanup
$ dune clean
$ cat from_spec_a.sexp
6
$ ls -l spec_a/**/*.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:16 spec_a/d1/1.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:16 spec_a/d1/2.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:16 spec_a/d1/3.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:32 spec_a/d2/1.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:32 spec_a/d2/2.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:32 spec_a/d2/3.txt
$ dune build @gen_spec_a
$ tree _build/default/spec_a
_build/default/spec_a
├── d1
│ ├── 1.txt
│ ├── 2.txt
│ └── 3.txt
└── d2
├── 1.txt
├── 2.txt
└── 3.txt
2 directories, 6 files
$ rm -rf spec_a/d2
$ dune build @gen_spec_a
$ ls -l spec_a/**/*.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:16 spec_a/d1/1.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:16 spec_a/d1/2.txt
-rw-r--r-- 1 louis louis 0 Aug 2 10:16 spec_a/d1/3.txt
$ tree _build/default/spec_a
_build/default/spec_a
├── d1
│ ├── 1.txt
│ ├── 2.txt
│ └── 3.txt
└── d2
├── 1.txt
├── 2.txt
└── 3.txt
2 directories, 6 files
$ cat from_spec_a.sexp
6