BundlePackages use a noop fetch strategy. The mirror logic was assuming
that the fetcher had a resource to cach after performing a fetch. This adds
a special check to skip caching if the stage is associated with a
BundleFetchStrategy. Note that this should allow caching resources
associated with BundlePackages.

When updating a mirror, Spack was re-retrieving all patches (since the
fetch logic for patches is separate). This updates the patch logic to
allow the mirror logic to avoid this.

Since cache_mirror does the fetch itself, it also needs to do the
checksum itself if it wants to verify that the source stored in the
mirror is valid. Note that this isn't strictly required because fetching
(including from mirrors) always separately verifies the checksum.

The targets for the cosmetic paths in mirrrors were being calculated
incorrectly as of fb3a3ba9: the symlinks used relative paths as targets,
and the relative path was computed relative to the wrong directory.

When creating a cosmetic symlink for a resource in a mirror, remove
it if it already exists. The symlink is removed in case the logic to
create the symlink has changed.

* Some packages (e.g. mpfr at the time of this patch) can have patches
  with the same name but different contents (which apply to different
  versions of the package). This appends part of the patch hash to the
  cache file name to avoid conflicts.
* Some exceptions which occur during fetching are not a subclass of
  SpackError and therefore do not have a 'message' attribute. This
  updates the logic for mirroring a single spec (add_single_spec)
  to produce an appropriate error message in that case (where before
  it failed with an AttributeError)
* In various circumstances, a mirror can contain the universal storage
  path but not a cosmetic symlink; in this case it would not generate
  a symlink. Now "spack mirror create" will create a symlink for any
  package that doesn't have one.

`spack module loads` and `spack module find` previously failed if any upstream modules were missing.  This prevented it from being used with upstreams (or, really, any spack instance) that blacklisted modules.

This PR makes module finding is now more lenient (especially for blacklisted modules).

- `spack module find` now does not report an error if the spec is blacklisted
  - instead, it prints a single warning if any modules will be omitted from the loads file
  - It comments the missing modules out of the loads file so the user can see what's missing
  - Debug messages are also printed so users can check this with `spack -d...`

- also added tests for new functionality

* Add a transaction around repeated calls to `spec.prefix` in the activation process
* cache the computation of home in the python package to speed up setting deps
* ensure that module-scope variables are only set *once* per module

`mirror_archive_path` was failing to account for the case where the fetched version isn't known to Spack.

- [x] don't require the fetched version to be in `Package.versions`
- [x] add regression test for mirror paths when package does not have a version

Fixes #13529
Fixes #13509

* remove reference to `spack.store` in method definition

Referencing `spack.store` in method definition will cache the `spack.config.config` singleton variable too early, before we have a chance to add command line and environment scopes.

Add a configuration option to suppress gpg warnings during binary
package verification. This only suppresses warnings: a gpg failure
will still fail the install. This allows users who have already
explicitly trusted the gpg key they are using to avoid seeing
repeated warnings that it is self-signed.

determine target relative to the link directory rather than the full link path (which includes the file name) (#13727)

Binaries with relative RPATHS currently do not relocate strings
hard-coded in binaries

This PR extends the best-effort relocation of strings hard-coded
in binaries to those whose RPATHs have been relativized.

If you do this in a spack environment:

    spack add hdf5+hl

hdf5+hl will be the root added to the `spack.yaml` file, and you should
really expect `hdf5+hl` to display as a root in the environment.

- [x] Add decoration to roots so that you can see the details about what
      is required to build.
- [x] Add a test.

This fixes a regression introduced in #10792.  `spack uninstall` in an
environment would not match concrete query specs properly after the index
hash of enviroments changed.

- [x] Search by DAG hash for specs to remove instead of by build hash

* environments: make shell modifications partially unconditional

* flake

* missing module name

* add regression test

* flake

* Make relative binaries relocate text files properly
* rb strings aren't valid in python 2
* move perl to new interface for setup_environment family methods

- [x] insert at beginning of list so fetch grabs local mirrors before remote resources
- [x] update the S3FetchStrategy so that it throws a SpackError if the fetch fails.  
      Before, it was throwing URLError, which was not being caught in stage.py.
- [x] move error handling out of S3FetchStrategy and into web_util.read_from_url()
- [x] pass string instead of URLError to SpackWebError

This changes Spack environments so that the YAML file associated with the environment is *only* written when necessary (i.e., if it is changed *by spack*).  The lockfile is still written out as before.

There is a larger question here of which part of Spack should be responsible for setting defaults in config files, and how we can get rid of empty lists and data structures currently cluttering files like `compilers.yaml`.  But that probably requires a rework of the default-setting validator in `spack.config`, as well as the code that uses `spack.config`.  This will at least help for `spack.yaml`.

* fix issue where spack.util.url.join() failed to correctly handle absolute path components
* add url util tests

This fixes a UnicodeDecodeError in the sbang patching function.

* Make package preferences a soft failure for targets, instead of a hard failure.
* Added unit tests for preferences expressed via packages.yaml

* Travis CI: Test Python 3.8

* Fix use of deprecated cgi.escape method

* Fix version comparison

* Fix flake8 F811 change in Python 3.8

* Make flake8 happy

* Use Python 3.8 for all test categories

Currently, query arguments in the Spack core are documented on the
Database._query method, where the functionality is defined.

For users of the spack python command, this makes the python builtin
method help less than ideally useful, as help(spack.store.db.query)
and help(spack.store.db.query_local) do not show relevant information.

This PR updates the doc attributes for the Database.query and
Database.query_local arguments to mirror everything after the first
line of the Database._query docstring.

* cuda: fix conflict statements for x86-64 targets

fixes #13462

This build system mixin was not updated after the support for specific
targets has been merged.

* Updated the version range of cuda that conflicts with gcc@8:

* Updated the version range of cuda that conflicts with gcc@8: for ppc64le

* Relaxed conflicts for version > 10.1

* Updated versions in conflicts

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* cpu: differentiate flags used for pristine LLVM vs. Apple's version

- configuration fails on newer versions when enabling sse/avx/avx2
- prefer an older version that will build with these features

remove this when issues are resolved with `trilinos^netcdf@4.7.2`