maint: simplify README to cover simple install instructions.

Remove instructions on how to install perl on different OS, there's
plenty of pages online on how to do it, nothing of this is BioPerl
specific.  Also link to the CPAN page about how to install perl
modules which applies to BioPerl modules.

Make reference to how BioPerl project is actually multiple
distributions and to install with cpanm by naming the module
required.

Add new HACKING.md, merge of README and INSTALL files, for users
interested in development.

HACKING.md

@@ -0,0 +1,256 @@
+# The Directory Structure
+
+The BioPerl directory structure is organized as follows:
+
+* **`Bio/`** - BioPerl modules
+
+* **`examples/`** - Scripts demonstrating the many uses of BioPerl
+
+* **`ide/`** - Files for developing BioPerl using an IDE
+
+* **`maintenance/`** - BioPerl housekeeping scripts
+
+* **`models/`** - DIA drawing program generated OO UML for BioPerl classes
+  (these are quite out-of-date)
+
+* **`scripts/`** - Useful production-quality scripts with POD documentation
+
+* **`t/`** - Perl built-in tests, tests are divided into subdirectories
+  based on the specific classes being tested
+
+* **`t/data/`** - Data files used for the tests, provides good example data
+
+* **`travis_scripts/`** - script to customize Travis
+
+# Documentation
+
+For documentation on BioPerl see the **HOWTO** documents online at http://bioperl.org/howtos.
+
+Useful documentation in the form of example code can also be found in the
+**`examples/`** and **`scripts/`** directories. The current collection includes
+scripts that run BLAST, index flat files, parse PDB structure files, make
+primers, retrieve ESTs based on tissue, align protein to nucleotide sequence,
+run GENSCAN on multiple sequences, and much more! See `bioscripts.pod` for a
+complete listing.
+
+Individual `*.pm` modules have their own embedded POD documentation as well. A
+complete set of hyperlinked POD, or module, documentation is available at
+http://www.bioperl.org/.
+
+Remember that '`perldoc`' is your friend. You can use it to read any file
+containing POD formatted documentation without needing any type of translator
+(e.g. '`perldoc Bio::SeqIO`').
+
+If you used the Build.PL installation, and depending on your platform, you may
+have documentation installed as man pages, which can be accessed in the usual
+way.
+
+# Releases
+
+BioPerl releases are always available from the website at http://www.bioperl.org/DIST or in CPAN. The latest code can be found at https://github.com/bioperl.
+
+* BioPerl currently uses a semantic numbering scheme to indicate stable release
+  series vs. development release series. A release number is a three digit
+  number like `1.2.0`.
+  * The *first digit indicates the major release*, the idea being that all the
+    API calls in a major release are reasonably consistent.
+  * The *second number is the release series*. This is probably the most
+    important number, and represents added functionality that is
+    backwards-compatible.
+  * The *third number is the point or patch release* and represents mainly bug
+    fixes or additional code that doesn't add significant functionality to the
+    code base.
+
+From the **1.0 release until the 1.6 release** even numbers (e.g. `1.4`) indicated stable releases. Stable releases were well tested and recommended for most uses. Odd numbers (e.g. `1.3`) were development releases which one would only use if one were interested in the latest features. The final number (e.g. in `1.2.1`) is the point or patch release. The higher the number the more bug fixes has been incorporated. In theory you can upgrade from one point or patch release to the next with no changes to your own code (for production cases, obviously check things out carefully before you switch over).
+
+The upcoming **1.7 release** will be the last release series to utilise the alternating 'stable'/'developer' convention. Starting immediately after the final 1.6 branch, we will start splitting BioPerl into several smaller easier-to-manage distributions. These will have independent versions, all likely starting with v1.7.0. **We do not anticipate major API changes in the 1.7.x release series, merely that the code will be restructured in a way to make maintenance more feasible.** We anticipate retaining semantic versioning until the 2.x release.
+
+# Caveats and Warnings
+
+When you run the tests with `./Build test` some tests may issue warnings messages or even fail. Sometimes this is because we didn't have anyone to test the test system on the combination of your operating system, version of perl, and associated libraries and other modules. Because BioPerl depends on several
+outside libraries we may not be able to test every single combination so if
+there are warnings you may find that the package is still perfectly useful.
+
+If you install the bioperl-run system and run tests when you don't have the
+program installed you'll get messages like `program XXX not found, skipping
+tests`. That's okay, BioPerl is doing what it is supposed to do. If you wanted
+to run the program you'd need to install it first.
+
+Not all scripts in the `examples/` directory are correct and up-to-date. If you find an issue with a script please submit a bug report to https://github.com/bioperl/bioperl-live/issues and consider helping out in their maintenance.
+
+If you are confused about what modules are appropriate when you try and solve a
+particular issue in bioinformatics we urge you to look at HOWTO documents first.
+
+# Module summary
+
+Here is a quick summary of many of the useful modules and how the
+toolkit is laid out.  Some of these are on their own distribution.
+
+All modules are in the `Bio::` namespace.
+
+* **`Seq`** is for *Sequences* (protein and DNA).
+    * `Bio::PrimarySeq` is a plain sequence (sequence data + identifiers)
+    * `Bio::Seq` is a fancier `PrimarySeq`, in that it has annotation (via
+    `Bio::Annotation::Collection`) and sequence features (via `Bio::SeqFeatureI` objects, attached via
+    `Bio::FeatureHolderI`).
+    * `Bio::Seq::RichSeq` is all of the above, plus it has slots for extra information specific to GenBank/EMBL/SwissProt files.
+    * `Bio::Seq::LargeSeq` is for sequences which are too big for
+    fitting into memory.
+
+* **`SeqIO`** is for *reading and writing Sequences*. It is a front end module
+  for separate driver modules supporting the different sequence formats
+
+* **`SeqFeature`** represent *start/stop/strand-based localised annotations (features) of sequences*
+    * **`Bio::SeqFeature::Generic`** is basic catchall
+    * **`Bio::SeqFeature::Similarity`** a similarity sequence feature
+    * **`Bio::SeqFeature::FeaturePair`** a sequence feature which is pairwise
+    such as query/hit pairs
+
+* **`SearchIO`** is for *reading and writing pairwise alignment reports*, like
+  BLAST or FASTA
+
+* **`Search`** is where the *alignment objects for `SearchIO` are defined*
+    * **`Bio::Search::Result::GenericResult`** is the result object (a blast
+    query is a `Result` object)
+    * **`Bio::Search::Hit::GenericHit`** is the `Hit` object (a query will have
+    0 to many hits in a database)
+    * **`Bio::Search::HSP::GenericHSP`** is the High-scoring Segment Pair
+    object defining the alignment(s) of the query and hit.
+
+* **`SimpleAlign`** is for *multiple sequence alignments*
+
+* **`AlignIO`** is for *reading and writing multiple sequence alignment
+  formats*
+
+* **`Assembly`** provides the start of an *infrastructure for assemblies* and
+  **`Assembly::IO`** *IO converters* for them
+
+* **`DB`** is the namespace for *all the database query classes*
+    * **`Bio::DB::GenBank/GenPept`** are two modules which query NCBI entrez for
+      sequences
+    * **`Bio::DB::SwissProt/EMBL`** query various EMBL and SwissProt
+      repositories for a sequences
+    * **`Bio::DB::GFF`** is Lincoln Stein's fast, lightweight feature and
+      sequence database which is the backend to his GBrowse system (see
+      www.gmod.org)
+    * **`Bio::DB::Flat`** is a fast implementation of the OBDA flat-file
+      indexing system (cross-language and cross-platform supported by O|B|F
+      projects see http://obda.open-bio.org).
+    * **`Bio::DB::BioFetch/DBFetch`** for OBDA, Web (HTTP) access to remote
+      databases.
+    * **`Bio::DB::InMemoryCache/FileCache`** (fast local caching of sequences
+      from remote dbs to speed up your access).
+    * **`Bio::DB::Registry`** interface to the OBDA specification for remote
+      data sources
+    * **`Bio::DB::Biblio`** for access to remote bibliographic databases.
+    * **`Bio::DB::EUtilities`** is the initial set of modules used for generic
+      queried using NCBI's eUtils.
+
+* **`Annotation`** collection of *annotation objects* (comments, DBlinks,
+  References, and misc key/value pairs)
+
+* **`Coordinate`** is a system for *mapping between different coordinate systems*
+  such as DNA to protein or between assemblies
+
+* **`Index`** is for *locally indexed flatfiles* with BerkeleyDB
+
+* **`Tools`** contains many *miscellaneous parsers and functions* for different
+  bioinformatics needs
+    * Gene prediction parser (Genscan, MZEF, Grail, Genemark)
+    * Annotation format (GFF)
+    * Enumerate codon tables and valid sequences symbols (CodonTable,
+    IUPAC)
+    * Phylogenetic program parsing (PAML, Molphy, Phylip)
+
+* **`Map`** represents *genetic and physical map representations*
+
+* **`Structure`** - parse and represent *protein structure data*
+
+* **`TreeIO`** is for reading and writing *Tree formats*
+
+* **`Tree`** is the namespace for **all associated Tree classes**
+    * **`Bio::Tree::Tree`** is the basic tree object
+    * **`Bio::Tree::Node`** are the nodes which make up the tree
+    * **`Bio::Tree::Statistics`** is for computing statistics for a tree
+    * **`Bio::Tree::TreeFunctionsI`** is where specific tree functions are
+      implemented (like `is_monophyletic` and `lca`)
+
+* **`Bio::Biblio`** is where *bibliographic data and database access objects*
+  are kept
+
+* **`Variation`** represent *sequences with mutations and variations* applied so one can compare and represent wild-type and mutation versions of a sequence.
+
+* **`Root`**, basic objects for the *internals of BioPerl*
+
+## The Test System
+
+The BioPerl test system is located in the `t/` directory and is
+automatically run whenever you execute the `./Build test` command.
+
+The tests have been organised into groups
+based upon the specific task or class the module being tested belongs
+to. If you want to investigate the behaviour of a specific test such as
+the Seq test you would type:
+
+```
+./Build test --test_files t/Seq/Seq.t --verbose
+```
+
+The `--test_files` argument can be used multiple times to try a set of test
+scripts in one go. The `--verbose` argument outputs the detailed test results, instead of just the summary you see during `./Build test`.
+
+The `--test-files` argument can also work as a glob. For instance, to run tests on all SearchIO modules, use the following:
+
+```
+./Build test --test_files t/SearchIO* --verbose
+```
+
+You can also use the command-line tool `prove` to run tests as well, which
+is quite useful if you are developing code:
+
+```
+prove -lrv t/SearchIO*
+```
+
+If you are trying to learn how to use a module, often the test suite
+is a good place to look. All good extreme programmers try and write a
+test BEFORE they write the module to insure that their module behaves
+the way they expect. You'll notice some `ok` and `skip` commands in a
+test, this is part of the Perl test suite that signifies a passed test
+with an 'ok N', where N is the test number. Alternatively you can tell
+Perl to skip tests. This is useful when, for example, your test
+detects that the network is not present and thus should skip, not
+fail, any tests that require a network connection.
+
+The core developers have indicated that future releases of BioPerl
+will require that new modules come with a test suite with some minimal
+tests.  Modules that lack adequate tests or could otherwise be
+considered 'unstable' will be moved into a separate developer
+distribution until adequate tests are added and the API stabilises.
+
+[how to install Docker]: https://docs.docker.com/engine/installation/
+[bioperl/bioperl]: https://hub.docker.com/r/bioperl/bioperl/
+[bioperl/bioperl-deps]: https://hub.docker.com/r/bioperl/bioperl-deps/
+
+# Using BioPerl via Docker
+
+If you don't have Docker installed already, instructions for [how to install Docker] on Linux, MacOSX, and Windows are available online.
+
+We officially support several builds (latest, stable, and releases)
+hosted in the [bioperl/bioperl] repo on Docker Hub. These images do not
+have a pre-defined entrypoint. If you have a BioPerl script in the
+current directory, you can run it as simple as this:
+
+```
+docker run -t --rm -v `pwd`:/work -w /work bioperl/bioperl perl my-script.pl
+```
+
+Or run an interactive shell:
+
+```
+docker run -ti --rm -v `pwd`:/work -w /work bioperl/bioperl bash
+```
+
+You can also build your own Docker image of BioPerl, using the same
+base image and pre-built dependencies that we use. Simply build off of
+the [bioperl/bioperl-deps] image.