* 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`

* docs: add a spack environment for building the docs

* docs: remove tutorial and link to spack-tutorial.readthedocs.io

The tutorial now has its own standalone website, versioned by instances
of the tutorial.  Link to that instead of versioning it directly with Spack.

Support mirroring all packages with `spack mirror create --all`.

In this mode there is no concretization:

* Spack pulls every version of every package into the created mirror.
* It also makes multiple attempts for each package/version combination
  (if there is a temporary connection failure).
* Continues if all attempts fail. i.e., this makes its best effort to
  fetch evrerything, even if all attempts to fetch one package fail.

This also changes mirroring logic to prefer storing sources by their hash
or by a unique name derived from the source.  For example:

* Archives with checksums are named by the sha256 sum, i.e.,
  `archive/f6/f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8.tar.gz`
  vs the previous `<package-name>-package-version>.tar.gz`
* VCS repositories are stored by a path derived from their URL,
  e.g. `git/google/leveldb.git/master.tar.gz`.

The new mirror layout allows different packages to refer to the same
resource or source without duplicating that download in the
mirror/cache. This change is not essential to mirroring everything but is
expected to save space when mirroring packages that all use the same
resource.

The new structure of the mirror is:

```
<base directory>/
  _source-cache/   <-- the _source-cache directory is new
    archive/       <-- archives/resources/patches stored by hash
      00/          <-- 2-letter sha256 prefix
        002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056.tar.gz
      01/
        0154c25c45b5506b6d618ca8e18d0ef093dac47946ac0df464fb21e77b504118.tar.gz
        0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea.tar.gz
        ...
    git/
      OpenFAST/
        openfast.git/
          master.tar.gz     <-- repo by branch name
      PHASTA/
        phasta.git/
          11f431f2d1a53a529dab4b0f079ab8aab7ca1109.tar.gz  <-- repo by commit
      ...
    svn/      <-- each fetch strategy has its own subdirectory
      ...
  openmpi/   <-- the remaining package directories have the old format
    openmpi-1.10.1.tar.gz  <-- human-readable name is symlink to _source-cache
```

In addition to the archive names as described above, `mirror create` now
also creates symlinks with the old format to help users understand which
package each mirrored archive is associated with, and to allow mirrors to
work with old spack versions. The symlinks are relative so the mirror
directory can still itself be archived.

Other improvements:

* `spack mirror create` will not re-download resources that have already
  been placed in it.

* When creating a mirror, the resources downloaded to the mirror will not
  be cached (things are not stored twice).

Restore upstream lock safety; avoid calling methods directly on upstream DB in test.