* module files tutorial : first complete draft

- first complete draft for module files tutorial
- minor corrections to module file reference

* module file tutorial : first batch of corrections

- module avail spelled out fully
- typos from @adamjstewart
- rewording of a few sentences

* module file tutorial : first batch of corrections

- emphasized lines in yaml files

* module file tutorial : fixes according to @citibeth and @adamjstewart reviews

- used long format for command options
- reworded unclear sentence on tokes
- reworked table in reference manual to make it clearer

* module file tutorial : implemented corrections collected on site from @schlyfts

* module file tutorial : removed comment (@hartzell suggestion)

* Add options for hashes, tree depth, and YAML to `spack spec`.

- Can now display hashes with `spack spec`, like `spack find`.
  - Removed the old "ids" argument to `spack spec` (which
    printed numerical values)b

- Can output YAML spec from `spack spec` with `-y`

- Can control depth of DAG traversal with --cover=[nodes|edges|paths]

- Can print install status (installed, missing, not installed) with -I

* Don't use YAML aliases in specs.

- Force Spack's YAML dumper to ignore aliases.
- aliases cause non-canonical YAML to be used in DAG hash, and result in
  redundant hashes.
- add a test to ensure this behavior stays

* remove obsolete instructions on hacking clang+gfortran

* add detailed instructions on how to setup Clang+gfortran on macOS

* spack install: forward sys.stdin to child processes fixes #2140

 - [ ] redirection process is spawned in __enter__ instead of __init__
 - [ ] sys.stdin is forwarded to child processes

* log: wrapped __init__ definition

* Fix style checker bug.

* spack flake8: print cwd-relative paths by default, with root-relative option.

1) list gfortran as a fc and f77 compiler that can work with clang
2) allow compatible gfortran to ./spack compiler find with clang by matching version numbers

This is based on the discussions in

https://github.com/LLNL/spack/issues/237
https://github.com/dealii/dealii/wiki/deal.II-in-Spack#mixing-gcc-and-clang-on-osx

This is not a long term solution but something to get us through the next months until the compiler
infrastructure is reworked to allow mixing and matching for C/C++ and Fortran compilers

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 1.5 hours

- Detailed debug information is now handed back to the parent process
  from builds, for *any* type of exception.

- previously this only worked for Spack ProcessErrors, but now it works
  for any type of error raised in a child.

- Spack will print an error message and source code context for build
  errors by default.

- It will print a stack trace when using `spack -d`, even when the error
  occurred in the child process.

- Ported old run-flake8-tests qa script to `spack flake8` command.
- New command does not modify files in the source tree
- Copies files to a temp stage modifies them there, and runs tests.
- Updated docs and `run-flake8-tests` script to call `spack flake8`.

- generalized and fixed to work with any key in YAML file
- simplified schema writing, as well
- add more unit tests for the config system
- Rename test/yaml.py to test/spack_yaml.py
  - Add test/yaml.pyc to ignored pyc files.

- Added new preferences to config.yaml:
  - source_cache
  - misc_cache
  - verify_ssl
  - checksum
  - dirty

- Moved temp finding logic to spack.stage
- Updated stage tests
- Added tests for new path substaitution of $user, $spack, $tempdir

- Added a schema for config.yaml
- Moved install tree configuration to config.yaml
- Moved etc/spack/install.yaml to etc/spack/defaults/config.yaml
- renamed install_area to "store", to use a term in common with guix/nix.
  - in `config.yaml` file, it's called the `install_tree` to be more
    intuitive to users.
  - `install_tree` might've worked in the code, but `install_tree` is
    already a global function in the spack namespace, from
    llnl.util.filesystem.

Merge #2030 added a cyclic dependency between the Cray platform needing
to read a `targets.yaml` config file and `config.py` needing to get the
platform names.

This commit removes the cyclic dependency in favor of the more general
config scheme. It also removes the now functionless `targets.yaml`
config file. This breaks 'frontend' targets on the Cray platform but
all architecture targets, including the frontend, that are provided by
CrayPE are added to the Platform anyway so users can be explicit about
the architecture targeted by the Cray compiler wrappers:

```
spack spec libelf arch=cray-CNL-frontend
```

becomes

```
spack spec libelf arch=cray-CNL-mc8         # on an XK7 or
spack spec libelf arch=cray-CNL-sandybridge # on an older XC30, etc..
```

The only way the 'frontend' target can be defined after this commit is
through target environment variables.

* module file support: major rework of docs

* module file support: fixed issues found by @adamjstewart

- list or enumeration should not be indented
- use console instead of bash or csh in things that are not scripts
- other typos

* module file support: fixed other issues found by @adamjstewart

- tables should not be indented
- substitute lines with pyobject to import an entire function
- get help output running commands
- typos

* module file support: fixes according to review comments

- @citibeth moved `spack module loads` after `spack load`
- @glennpj tried to clarify installation table + changes to language
- @tgamblin Removed top level section and moved the whole thing into the reference manual

* module file support: moved directive before spack module loads

- enable keyword works again
- test/modules.py : proper clean-up after tests

External packages do not have an spec.yaml file so don't check for it.
Without this change any time a package depends on an external package
when the new package is installed you will get the error

Install prefix exists but contains no spec.yaml

This problem has also haunted me since I started using Spack since PETSc
depends on Python and I used an external python but fortunately it
was relatively easy to debug once I could reproduce it at will.

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 1 hour

Fixes #1845

This replaces a custom token-based substitution format with calls to
Spec.format in modules.py

This also resolves a couple issues:

- LmodModules set configuration globally instead of in its initializer
  which meant test-specific configuration was not applied
- Added support for setting hash_length=0 for LmodModules. This only
  affects the module filename and not the directory names for the
  hierarchy tokens in the path. This includes an additional unit test.

The breaks `spack create`.

Removed documentation on false paths as per #2083

* document recommended usage of system blas/lapack

* update doc

* minor

* reword

* spack install : added --log-format option (incorporates test-install command)

fixes #1907

* qa : removed extra whitespace

* add filter_system_paths()

* filter system paths in set_build_environment_variables()

* two function: lib/inc + bin

* reverse order in bin

* fix order

* minor

* improvements of the code

* more cleanup

* alternative solution for filter_bins

* fiddle base alalazo's approach

* minor

* minor