remove deprecated documentation files

config/*.reference and doc/man/* are out-of-date and redundant since
the provided documentation is available in doc/rst/.

3 files changed, 0 insertions, 614 deletions

diff --git a/config/R-overlay.conf.reference b/config/R-overlay.conf.reference
deleted file mode 100644
index 067e1a7..0000000
--- a/config/R-overlay.conf.reference
+++ /dev/null
@@ -1,342 +0,0 @@
-# R-overlay.conf
-#  This file explains how to write a R overlay main config,
-#  it can also be used as config file.
-#
-# -- Table of contents --
-#
-# 1  -- config value types and file syntax
-# 2  -- config quickstart (basic overview of options to set)
-# 3  -- config entries
-#  a -- misc
-#  b -- overlay
-#  c -- other config files
-#  d -- logging
-#  e -- other (debugging, testing, ...)
-#
-# -- end of ToC --
-
-# = config value types and file syntax =
-
-# This file is parsed using shlex (shell-like syntax)
-#  * '#' is the comment char
-#  * variables ("${X}") are not supported
-#  * whitespace is ignored (in most cases)
-#    => whitespace in file paths is generally not supported,
-#        but may work with some restrictions
-#  * quotes are optional, but allow to span long values over multiple lines,
-#    e.g. <<
-# SIMPLE_RULES_FILE="<path to first rule file>
-# <another one>
-# "
-#    >>
-#
-#
-# some options have value type restrictions,
-#
-# special value types used in this config ("* allowed values: <type>"):
-#
-#  log level -- choose from {DEBUG, INFO, WARN, WARNING, ERROR, CRITICAL}
-#  bool      -- string that represents a boolean value,
-#                true  := {y,yes,on,1,true,enabled}
-#                false := {n,no,off,0,false,disabled}
-#                other values are not allowed
-#
-#
-# implicit value types:
-#
-# list       -- option has multiple values separated by whitespace,
-#                use quotes to specify more than one value
-#
-# file, dir  -- value will be expanded ( ~ => ${HOME}, x => ${PWD}/x etc.),
-#                value has to be a file (or dir) if it exists
-#
-# <empty>    -- often leads to errors (in case of value type restrictions),
-#                just comment out config entries
-#
-#
-#
-# "*** NOT IN USE ***" means that an option is read and integrated into
-# the config tree, but never used (normal entry in config/entrymap).
-#  => value will be validated
-#
-# "*** <option> is not available> ***" means that an option is read, but
-#  ignored ("None" entry in config/entrymap).
-#  => value won't be validated
-
-
-# = config quick start =
-# This is a listing of options to consider
-#
-# options that are required:
-#  OVERLAY_NAME,      (or use --overlay-name <name>)
-#  OVERLAY_DIR,       (or use --overlay <OVERLAY>)
-#  DISTFILES,         (or use --distroot <DISTROOT>)
-#  REPO_CONFIG,       (or use --repo-config <file>) # FIXME: required?
-#  FIELD_DEFINITION   (or use --field-definition <file>)
-#
-# options that are optional but essential for a usable result:
-#  OVERLAY_ECLASS,
-#  SIMPLE_RULES_FILE  (or use --deprule-file <file>)
-#
-# some options for logging:
-#  LOG_CONSOLE,
-#  LOG_FILE,
-#  LOG_LEVEL,
-#  LOG_LEVEL_FILE,
-#  LOG_LEVEL_CONSOLE
-#
-# some options for debugging and testing:
-#  LOG_FILE_UNRESOLVABLE,
-#  DESCRIPTION_DIR
-#
-
-
-# = config starts here =
-
-# == misc options ==
-
-# DISTFILES_ROOT
-#  the root directory of repo distdirs
-#   Repos will create their distdirs in this directory unless
-#   they specify another location.
-#  * alias: DISTDIR, DISTFILES
-#  * defaults to <unset> (but required!)
-#DISTFILES_ROOT = "distfiles-root"
-
-
-# == overlay options ==
-
-# OVERLAY_NAME
-#  name of the overlay
-#  * defaults to <unset> (but required!)
-#OVERLAY_NAME = "ROverlay"
-
-# OVERLAY_DIR
-#  overlay root directory
-#   This is the directory where the overlay content, e.g. ebuilds and
-#   profiles/repo_name will be written into.
-#  * defaults to <unset> (but required!)
-#OVERLAY_DIR = "overlay-root"
-
-# OVERLAY_ECLASS
-#  eclass files to import into the overlay and us in ebuilds
-#   Note that overlay creation fails if importing any of the
-#   specified eclass files fails.
-#  * accepted values: a list of files that end with '.eclass' or
-#     don't have an extension
-#  * defaults to <unset> (empty list) - this is NOT useful
-#  * alias: ECLASS
-#OVERLAY_ECLASS = "eclass/R-packages.eclass"
-
-# OVERLAY_CATEGORY
-#  overlay category of the created ebuilds
-#  * accepted values: no restrictions made, but don't insert a '/'!
-#  * defaults to sci-R
-#OVERLAY_CATEGORY = 'dev-R'
-
-# OVERLAY_KEEP_NTH_LATEST
-#  keep the n-th latest ebuilds per R package, removing all others
-#  * accepted values: integer, has no effect if < 1
-#  * defaults to <unset>, which disables this option (keep all ebuilds)
-#OVERLAY_KEEP_NTH_LATEST = 3
-
-# EBUILD_HEADER
-#  ebuild header file that will be included in all created ebuilds
-# *** NOT IN USE ***
-#EBUILD_HEADER = "ebuild_header.txt"
-
-# OVERLAY_MANIFEST_IMPLEMENTATION
-#  Manifest implementation to be used
-#   Currently, there's only one implementation available, manifest
-#   writing using the ebuild(1) executable.
-#   * accepted values:
-#   -> 'default'         -- use the default implementation
-#   -> 'none'            -- do not use any implementation,
-#                           this leads to runtime errors
-#                           whenever write_manifest() is called
-#   -> 'external:ebuild' -- generate Manifest files using ebuild(1)
-#
-#  * defaults to 'default'
-#  * alias: MANIFEST_IMPLEMENTATION
-
-# == other config files ==
-
-# some config options are split from this file for various reasons:
-# * no need to be modifed by users (in most cases)
-#  -> FIELD_DEFINITION
-# * special syntax that is not compatible with this file
-#  -> SIMPLE_RULES_FILE
-# * special syntax that eases adding/reading entries (-> all)
-# * config is independent from this file
-#  -> e.g. per-repo script runs using the same main config ("-R <file>" option)
-
-
-# FIELD_DEFINITION
-#  path to the config file that controls DESCRIPTION file reading
-#  * defaults to <unset> (but required!)
-#  * alias: FIELD_DEFINITION_FILE
-#FIELD_DEFINITION = "description_fields.conf"
-
-# REPO_CONFIG
-#  path to the repo config file
-#   Please see the example file for file format.
-#  * defaults to <unset> (but required!)
-#  * alias: REPO_CONFIG_FILE, REPO_CONFIG_FILES
-#REPO_CONFIG = "repo.list"
-
-# SIMPLE_RULES_FILE
-#  list of (simple) dependency rule files or dirs
-#   Please see the rule example file for file format.
-#   Directories will be non-recursively scanned for files.
-#   Files can also be compressed, either bzip2 (.bz2 file ext) or gzip (.gz)
-#  * defaults to <unset>, which effectively disables dependency resolution
-#     since no other dependency resolution methods are available.
-#     This gives poor results!
-#  * alias: SIMPLE_RULES_FILES
-#SIMPLE_RULES_FILE = "simple-deprules.d/R"
-
-# == logging ==
-
-# LOG_ENABLED
-#  enable/disable logging (globally)
-#  * accepted values: bool
-#  * defaults to enabled => use per-log target settings, e.g. LOG_CONSOLE
-#LOG_ENABLED = "no"
-
-# LOG_LEVEL
-#  the default log level
-#   Choices are DEBUG, INFO, WARN, WARNING, ERROR, CRITICAL.
-#  * defaults to <unset>, which causes console/file logging
-#     to use their own defaults
-#LOG_LEVEL = DEBUG
-
-# LOG_DATE_FORMAT
-#  date format used in logging
-#  * defaults to '%F %H:%M:%S'.
-#LOG_DATE_FORMAT = '%a, %H:%M'
-
-# *** LOG_FORMAT is not available ***
-
-
-# === console logging ===
-
-# LOG_CONSOLE
-#  enable/disable logging to console
-#  * accepted values: bool
-#  * defaults to enabled
-#  * alias: LOG_CONSOLE_ENABLED
-#LOG_CONSOLE = "no"
-
-# LOG_FORMAT_CONSOLE
-#  log format used in console logging
-#  * defaults to '%(levelname)-8s %(name)-14s: %(message)s'
-#  * alias: LOG_CONSOLE_FORMAT
-#LOG_FORMAT_CONSOLE = '[%(name)s] %(message)s'
-
-# LOG_LEVEL_CONSOLE
-#  log level for console logging, see LOG_LEVEL
-#  * accepted values: a log level
-#  * defaults to INFO
-#  * alias: LOG_CONSOLE_LEVEL
-#LOG_LEVEL_CONSOLE = "DEBUG"
-
-# *** LOG_CONSOLE_STREAM is not available ***
-
-
-# === file logging ===
-
-# LOG_FILE
-#  log file to write
-#   File logging will be disabled if left blank / commented out.
-#  * defaults to <unset>
-#LOG_FILE = ""
-
-# LOG_LEVEL_FILE
-#  log level used in file logging
-#  * accepted values: a log level, see LOG_LEVEL
-#  * defaults to: WARNING
-#  * alias: LOG_FILE_LEVEL
-#LOG_LEVEL_FILE = "ERROR"
-
-# LOG_FORMAT_FILE
-#  log format used in file logging
-#  * defaults to '%(asctime)s %(levelname)-8s %(name)-10s: %(message)s'
-#  * alias: LOG_FILE_FORMAT
-#LOG_FORMAT_FILE = '%(asctime)s $(levelname)s [%(name)s]: %(message)s'
-
-# LOG_FILE_ROTATE
-#  enable/disable log file rotation
-#   The log file will be rotated on every script run.
-#  * accepted values: bool
-#  * defaults to disabled
-#LOG_FILE_ROTATE = "yes"
-
-# LOG_FILE_ROTATE_COUNT
-#  number of rotated log files to keep
-#   Only used when log file rotation is enabled.
-#  * accepted values: int (make sure it's >= 0)
-#  * defaults to 3
-#LOG_FILE_ROTATE_COUNT = 10
-
-# LOG_FILE_BUFFERED
-#  buffer log entries in memory before writing them to the log file
-#   This should reduce I/O blocking when using low log levels with threads.
-#  * accepted values: bool
-#  * defaults to enabled
-#LOG_FILE_BUFFERED = "no"
-
-# LOG_FILE_BUFFER_COUNT
-#  max number of log entries to buffer
-#   Only used when log entry buffering is enabled.
-#  * accepted values: integer (make sure that the value is >= 1)
-#  * defaults to 250
-#  * alias: LOG_FILE_BUFFER_CAPACITY
-#LOG_FILE_BUFFER_COUNT = 50
-
-# LOG_FILE_ENABLED
-#  enable/disable logging to file
-#  * accepted values: bool
-#  * defaults to enabled (which grants LOG_FILE control over this setting)
-#LOG_FILE_ENABLED = "no"
-
-
-# == options for debugging, (manual) dependency rule creation, testing, ... ==
-
-# LOG_FILE_UNRESOLVABLE
-#  file where unresolved dependency strings will be written to
-#   Useful if you want to create new rules,
-#    run -> read unresolvable file -> create rules -> rerun.
-#   Comment out to disable.
-#  * defaults to <unset>
-#LOG_FILE_UNRESOLVABLE = "log/dep_unresolvable.log"
-
-# LOG_FILE_RESOLVED
-#  file where resolved dep strings will be written to
-#  *** NOT IN USE ***
-#LOG_FILE_RESOLVED = ""
-
-# DESCRIPTION_DIR
-#  directory where description files will be written into
-#   If enabled: write all read description files to
-#     <descfiles dir>/<R package name>_<R package version>.desc
-#   Comment out to disable.
-#  * defaults to <unset>
-#  * alias: DESCRIPTION_DESCFILES_DIR
-#DESCRIPTION_DIR = "desc-files"
-
-# EBUILD_PROG
-#  name of/path to the ebuild executable
-#  * accepted values: no restrictions made,
-#     but overlay writing will fail if the value is invalid,
-#     which is a huge time loss since ebuilds have been created before writing.
-#  * defaults to "ebuild"
-#EBUILD_PROG = "/usr/local/bin/ebuild"
-
-# RSYNC_BWLIMIT
-#  set a max. average rsync bandwidth usage (in kilobytes/second)
-#   This is a per-"rsync command" setting using rsync's "--bwlimit" option
-#   Note: you can set per-repo bwlimit's in the repo config file
-#    TODO-note: ^ make sure that this option doesn't interfere
-#  * accepted values: int (>0 expected)
-#  * defaults to <unset>
-#RSYNC_BWLIMIT = 10000
diff --git a/config/repo.list.reference b/config/repo.list.reference
deleted file mode 100644
index 378c03e..0000000
--- a/config/repo.list.reference
+++ /dev/null
@@ -1,105 +0,0 @@
-# repo.list
-#  This file explains how to write repo config files.
-
-# !! out of date, see man/roverlay-repo.5
-
-# This file is parsed used ConfigParser syntax (known from .ini files).
-
-# A repo entry describes
-# * where to find R packages that will be used for overlay creation,
-#    and optionally where and how to get the R packages (using repo types)
-# * how ebuilds can download the R packages (=> SRC_URI)
-
-# Each repository is introduced with [<section name>] and has to declare
-# some options.
-#
-# general options are:
-#
-# * required:
-#
-#   src_uri   -- this is used to determine the SRC_URI in ebuilds
-#                 (SRC_URI=<src_uri>/<package file name>)
-#                 FIXME note: check that subdirs are handled correctly
-#
-# * optional:
-#
-#   name      -- name of the repository
-#                 optional, defaults to <section name>
-#   type      -- the type of this repo, see below
-#                 optional, defaults to rsync
-#   directory -- the local package directory,
-#                 optional, defaults to <DISTFILES ROOT (from config)>/<name>
-#
-#   (base_uri -- don't use, to be removed)
-#
-#
-# There are two types of repos, "rsync" and "local" ones:
-#
-# * Local repo;
-#   A Local repo represents a directory with R packages in it.
-#   It will never be modified (i.e. synced) and has no special options.
-#
-# * Rsync repo:
-#   An Rsync repo uses a local directory to sync with a remote.
-#   Its directory will be modified whenever syncing (using the rsync program).
-#   Behaves like a local repo if syncing is disabled.
-#
-#  default rsync options (always passed to rsync):
-#   --links, --safe-links, --times, --compress, --dirs, --prune-empty-dirs,
-#   --force, --delete, --human-readable, --stats, --chmod=ugo=r,u+w,Dugo+x
-#
-#  This type has special options:
-#
-#  rsync_uri        -- required, rsync uri
-#  recursive        -- optional, passes '--recursive' to rsync
-#                       if this option is set to 'yes'
-#  extra_rsync_opts -- optional options to pass to rsync, this
-#                       can be used to exclude/include files,
-#                       show progress while syncing etc.
-#                       Note: options cannot contain whitespace! (#FIXME note: this could be allowed if useful)
-#
-#
-
-
-# == Repo entry examples ==
-
-# a local directory with packages in /var/www/R_packages
-#
-#[local_packages]
-#type      = local
-#src_uri   = http://localhost/R_packages
-#directory = /var/www/R_packages
-
-
-# a local directory with packages manually downloaded from CRAN
-# * directory will be automatically set to <DISTROOT>/CRAN/selected
-#
-#[CRAN/selected]
-#type    = local
-#src_uri = http://cran.r-project.org/src/contrib
-
-# CRAN rsync repo
-# * type will be set to rsync
-# * directory will be set to <DISTROOT>/CRAN/all
-# * rsync progress will be shown during transfer
-# * not recursive, the package archive and R release won't be fetched
-# * this needs about 2.5G disk space
-#
-#[CRAN/all]
-#src_uri   = http://cran.r-project.org/src/contrib
-#rsync_uri = cran.r-project.org::CRAN/src/contrib
-#extra_rsync_opts = --progress
-
-# CRAN rsync repo (selective transfer)
-# * type is explicitly set to rsync
-# * only packages starting with "r" or "R" will be fetched
-# * directory will be set to <DISTROOT>/CRAN/only_letter_R
-# * rsync progress will be shown during transfer
-# * not recursive
-# * this needs about 300M disk space
-#
-#[CRAN/only_letter_R]
-#type      = rsync
-#src_uri   = http://cran.r-project.org/src/contrib
-#rsync_uri = cran.r-project.org::CRAN/src/contrib
-#extra_rsync_opts = --include=r* --include=R* --exclude=* --progress
diff --git a/config/simple-deprules.conf.reference b/config/simple-deprules.conf.reference
deleted file mode 100644
index 3c15bac..0000000
--- a/config/simple-deprules.conf.reference
+++ /dev/null
@@ -1,167 +0,0 @@
-#! NOPARSE
-#
-# simple dependency rules file
-#
-# This file has been replaced by the dep rule files in simple-deprules.d/,
-# but explains the syntax.
-#
-# === Syntax ===
-#
-# You can specify single and multiline rules here,
-#  the basic syntax is "<portage identifier> <matches> <keyword(s)>".
-#
-#
-# There are two types of dependency string matching:
-#  standard : a dep string has to match exactly
-#              "R(>=2.15)" != "R" => UNRESOLVABLE
-#
-#  fuzzy    : the resolver will try to find a match using string
-#              interpolation/metrics
-#               "R(>=2.15)" ~ "R" => ">=dev-lang/R-2.15"
-#               "R(!=2.15)" ~ "R" => "(!dev-lang/R-2.15 dev-lang/R)"
-#               "R(>=2.15)" % "R" => <ignored> (% is fuzzy ignore)
-#
-#
-# a single line entry looks like
-## (1)  <portage package> :: <dependency string>  (standard simple dep)
-## (2) ~<portage package> :: <dependency string>  (fuzzy simple dep)
-## (3)  <dependency string>                       (standard selfdep)
-## (4) ~<dependency string>                       (fuzzy selfdep)
-## (5) ! :: <dependency string>                   (standard ignored dep)
-## (6) % :: <dependency string>                   (fuzzy ignored dep)
-#
-# Dependency strings are case-insensitive.
-#
-# (3) and (4) are shortcuts for [~]<overlay category>/<dep> :: <dep>,
-#  e.g. "fftw" matches "fftw" and resolves to "sci-R/fftw".
-#  This is useful 'cause you don't have to use a hardcoded overlay category
-#  here.
-# (5) and (6) are ways to define deps that should be ignored
-#  (=resolved to nothing). They're identical to (1)/(2), but use ! / % as
-#  portage package.
-#
-#
-# a multiline entry looks like
-## [~]<portage package> {
-## <dependency string 1>
-## <dependency string 2>
-## ...
-## <dependency string n>
-## }
-#
-# selfdeps cannot be declared in a multiline rule
-#
-# The precedence order of the rules in this file is
-## single line ignore > single line > multi line ignore > multi line
-#### this has to be fixed in the dep rule reader
-#
-# Note:
-# * you cannot write comments in a multiline rule, writing
-## dev-lang/R {
-##  # the following dep should resolve to R
-##  R(>= 2.15.0)
-## }
-# means that both strings '# the following dep should resolve to R' and
-# 'R(>= 2.15.0)' resolve to 'dev-lang/R'!
-#
-# * compound portage dependency statements (man 5 ebuild) are supported,
-#   but only in standard simple deps, e.g.
-## || ( <dev-lang/R-2.14.0 >dev-lang/R-2.14.0 ) :: R (!= 2.14.0)
-#
-#
-
-# === Examples ===
-
-# == single line entries ==
-
-# = standard simple dep =
-# this rule matches 'R (>= 2.15.0)' and resolves it as 'dev-lang/R-2.15.0'
-dev-lang/R-2.15.0 :: R (>= 2.15.0)
-
-# = fuzzy simple dep =
-
-# this rule matches
-## (a) R <version modifier?> <version>
-## (b) R (<version modifier?> <version>)
-## (c) R [<version modifier?> <version>]
-## (d) R {<version modifier?> <version>}
-## (e) R
-# variant (a) is whitespace sensitive (>= 1 whitespace char between R and
-# the version modifier/version), the others ignore all whitespace chars.
-# variant (e) is the standard simple rule behaviour.
-#
-# the dep string is then resolved as <version modifier?>dev-lang/R-<version>
-#
-# version modifier is optional and can be one out of {>=, <=, >, <, !=, =, ! },
-# where ! / != are being resolved a 'specific version is forbidden'.
-# '>=' is assumed as version modifier if it is left out and a specific version
-# is required.
-#
-# examples matches:
-# (a) r 2.13       -> >=dev-lang/R-2.13
-# (b) R(>= 2.14)   -> >=dev-lang/R-2.14
-# (c) R [<2.10]    -> <dev-lang/R-2.10
-# (d) r{  !2.12 }  -> ( !=dev-lang/R-2.12 dev-lang/R )
-# (e) R            -> dev-lang/R
-#
-~dev-lang/R :: R
-
-# = standard selfdep =
-# resolves "tuneR","tuner",.. as "sci-R/tuneR"
-tuneR
-
-# = fuzzy selfdep =
-# * see fuzzy simple dep
-# example match: resolves "zoo 1.10" as ">=sci-R/zoo-1.10"
-~zoo
-
-# = standard ignored dep =
-# ignores "R"
-! :: R
-
-# = fuzzy ignored dep =
-# ignores everything that fuzzy-matches R (see fuzzy simple dep)
-% :: R
-
-# == multi line entries ==
-
-# = simple multiline rule =
-# matches "R (>= 2.15)", "R" and resolves them as dev-lang/R
-dev-lang/R {
-	R (>= 2.15)
-	R
-}
-
-# = fuzzy multiline rule =
-~dev-lang/R {
-	R
-	the R programming language
-}
-
-# = ignored dep multiline rule =
-# equals ! :: see README
-! {
-	see README
-}
-
-# = fuzzy ignored dep multiline rule =
-# equals % :: R
-% {
-	R
-}
-
-# === Extra ===
-
-# There's a special keyword that tells the rule reader to stop parsing,
-# see line #1. It has to be exactly '#! NOPARSE' or '#! BREAK', with no
-# additional content at the end of the line.
-#! NOPARSE
-#! BREAK
-
-# There's also a keyword to set the dependency type (sys, pkg or all),
-# the syntax is '#deptype <type>'.
-#deptype sys
-#deptype pkg
-#deptype all
-
-