previously, the prefix wasn't added to PYTHONPATH because it didn't exist yet at build-time
this fixes python package import tests, see https://github.com/spack/spack/issues/45801

Spack's spec hashing mechanism considers only build, link, and run dependencies, overlooking test dependencies. As a result, although Spack correctly concretizes environments when `--test root` is specified (including test dependencies), the resulting lockfile dict only includes the deps whose types affect the hash (build/link/run) and when the env is loaded, test dependencies are not, and tests fail. The workaround suggested in the Spack issue [here](https://github.com/spack/spack/issues/29447) is deleting the lockfile every time and allowing `spack install --test root` to recreate it. By extending Spack's default hash type to include test dependencies, the need for this workaround is eliminated and concretization and installation can be split into separate steps.

* Fix hash change due to None vs {}

* Enforce null for empty list of external_modules

* e4s cray rhel ci stack: re-enable and update for new cpe, should fix cray libsci issue

* only run e4s-cray-rhel stack

* Mkae Autotools build_system point at correct build_directory

* remove selective enable of cray-rhel stacks

* restore SPACK_CI_DISABLE_STACKS

* use dot prefix to hide cray-sles jobs instead of comment-out

---------

Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>

fixes a bug where `x86_64:` and `ppc64le:` intersected, and x86_64: and :haswell did not.

Since macOS 15 `ld -single_module` warns with a deprecation message,
which makes configure scripts believe the flag is unsupported. That
in turn triggers a code path where `archive_cmds` is set to

```
$CC -r -keep_private_externs -nostdlib ... -dynamiclib
```

instead of just

```
$CC -dynamiclib ...
```

This code path was meant to trigger only on ancient macOS <= 14.4 where
libtool had to add `-single_module`, which is the default since macos
14.4, and is now apparently deprecated because the flag is a no-op for
more than 15 years.

The wrong `archive_cmds` causes actual problems combined with a bug in
OpenMPI's compiler wrapper (`CC=mpicc`), which appends `-rpath` flags,
which cause an error when combined with the `-r` flag added by the
autotools.

Spack's compiler wrapper doesn't do this, but it's likely there are
other compiler wrappers out there that are not aware that `-r` and
`-rpath` cannot be combined.

The fix is to change defaults: `lt_cv_apple_cc_single_mod=yes`.

`kcov` was removed in Ubuntu 24.04, and it is no longer
installable via `apt` in our CI images. Instal it via
Linuxbrew instead, at least until it comes back to Ubuntu.

`subversion` is also not installed on ubuntu 24 by default,
so we have to install it manually.

- [x] Add linuxbrew to linux tests
- [x] Install `kcov` with brew
- [x] Install subversion with `apt`

Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>

* filter_file: make tempfile later

* also add a `.` after the filename

* `f.tell` on a `TextIOWrapper` does not return the offset in bytes, but
  an opaque integer that can only be used for `f.seek` on the same
  object. Spack assumes it's a byte offset.
* Do not open in a locale dependent way, but assume utf-8 (and allow
  users to override that)
* Use tempfile to generate a backup/temporary file in a safe way
* Comparison between None and str is valid and on purpose.

ensure that CMAKE_INSTALL_RPATH_USE_LINK_PATH=ON works in qt packages.

Automatic splicing say `Spec` grow a `__len__` method but it's only used
in one place and it's not clear the semantics are useful elsewhere. It also
runs the risk of Specs one day being confused for other types of containers.

Rather than introduce a new function for one algorithm, let's use a more
specific method in the splice code.

- [x] Use topological ordering in `_resolve_automatic_splices` instead of 
      sorting by node count
- [x] delete `Spec.__len__()` and `Spec.__bool__()`

---------

Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Greg Becker <becker33@llnl.gov>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

`spack spec` output has looked like this for a while:

```console
> spack spec /v5fn6xo /wd2p2v7
Input spec
--------------------------------
 -   /v5fn6xo

Concretized
--------------------------------
[+]  openssl@3.3.1%apple-clang@16.0.0~docs+shared build_system=generic certs=mozilla arch=darwin-sequoia-m1
[+]      ^ca-certificates-mozilla@2023-05-30%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
...

Input spec
--------------------------------
 -   /wd2p2v7

Concretized
--------------------------------
[+]  py-six@1.16.0%apple-clang@16.0.0 build_system=python_pip arch=darwin-sequoia-m1
[+]      ^py-pip@23.1.2%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
```

But the input spec is right there on the CLI, and it doesn't add anything to the output.
Also, since #44843, specs concretized in the CLI line can be unified, so it makes sense
to display them as we did in #44489 -- as one multi-root tree instead of as multiple
single-root trees.

With this PR, concretize output now looks like this:

```console
> spack spec /v5fn6xo /wd2p2v7
[+]  openssl@3.3.1%apple-clang@16.0.0~docs+shared build_system=generic certs=mozilla arch=darwin-sequoia-m1
[+]      ^ca-certificates-mozilla@2023-05-30%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[+]      ^gmake@4.4.1%apple-clang@16.0.0~guile build_system=generic arch=darwin-sequoia-m1
[+]      ^perl@5.40.0%apple-clang@16.0.0+cpanm+opcode+open+shared+threads build_system=generic arch=darwin-sequoia-m1
[+]          ^berkeley-db@18.1.40%apple-clang@16.0.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=darwin-sequoia-m1
[+]          ^bzip2@1.0.8%apple-clang@16.0.0~debug~pic+shared build_system=generic arch=darwin-sequoia-m1
[+]              ^diffutils@3.10%apple-clang@16.0.0 build_system=autotools arch=darwin-sequoia-m1
[+]                  ^libiconv@1.17%apple-clang@16.0.0 build_system=autotools libs=shared,static arch=darwin-sequoia-m1
[+]          ^gdbm@1.23%apple-clang@16.0.0 build_system=autotools arch=darwin-sequoia-m1
[+]              ^readline@8.2%apple-clang@16.0.0 build_system=autotools patches=bbf97f1 arch=darwin-sequoia-m1
[+]                  ^ncurses@6.5%apple-clang@16.0.0~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=darwin-sequoia-m1
[+]                      ^pkgconf@2.2.0%apple-clang@16.0.0 build_system=autotools arch=darwin-sequoia-m1
[+]      ^zlib-ng@2.2.1%apple-clang@16.0.0+compat+new_strategies+opt+pic+shared build_system=autotools arch=darwin-sequoia-m1
[+]          ^gnuconfig@2022-09-17%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[+]  py-six@1.16.0%apple-clang@16.0.0 build_system=python_pip arch=darwin-sequoia-m1
[+]      ^py-pip@23.1.2%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[+]      ^py-setuptools@69.2.0%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
[-]      ^py-wheel@0.41.2%apple-clang@16.0.0 build_system=generic arch=darwin-sequoia-m1
...
```

With no input spec displayed -- just the concretization output shown as one consolidated
tree and multiple roots.

- [x] remove "Input Spec" section and "Concretized" header from `spack spec` output
- [x] print concretized specs as one BFS tree instead of multiple

---------

Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>

benchmarked to test if that is a correct decision.