When adding an Environment to a user's shell, Spack was only adding
root specs. This now includes run dependencies of root specs.

Partially undoes spack#23485

The current logic of `spack env activate` is as follows:

1. collect root specs
2. add root specs + transient run type deps of root specs to a list
3. call `environment_modifications_for_spec` for every spec of this list

However, `environment_modifications_for_spec` also processes run type
dependencies of the spec, so we're doing a lot of redundant work,
resulting in O(n^2) calls to `modifications_from_dependencies` if we
have a chain of deps `a` <- `b` <- ... <- `z` of deptype `run`.

This PR drops step 2, so that we call
`environment_modifications_for_spec` only on the root specs, and this
function will process the run type for us anyways.

Given an environment like this:

```yaml
spack:
  specs:
  - py-flake8
  - py-matplotlib
  - py-isort
  - py-sphinx
  - py-six
  - py-ipython
```

This is the time spent on `activate` before and after:

**Before**:

```
In [1]: from spack.main import SpackCommand
In [2]: env = SpackCommand('env')
In [3]: %timeit env('activate', '--sh', '.')
2.56 s ± 11.4 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
```

**After**:

```
In [1]: from spack.main import SpackCommand
In [2]: env = SpackCommand('env')
In [3]: %timeit env('activate', '--sh', '.')
761 ms ± 4.36 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
```

which is 70% less.