Resolve the function mapping, split two long pages, and fix 3.0.0b1 install instructions

[edkerk]

Two rounds of feedback: resolving every unmapped function in the MATLAB vs Python table, then splitting two pages that had grown too long and fixing the install instructions to actually install the pre-release this site documents.

All 63 RAVEN functions with no recorded Python counterpart, checked individually against the tracked raven-toolbox source (build-validated, so a wrong name fails the build) and, where the guide pages already answered it, against their own function tables.

• 12 are real counterparts under a different name (gapFillFastCore and
  gapFillSwiftCore both map to fill_gaps_fast_lp, which implements both
  algorithms behind a method= argument; replaceMets to replace_metabolite;
  the rest were already answered by a guide page's own function table).

• 13 are covered by cobrapy directly, most already stated in a guide page
  (addMets, addExchangeRxns, getAllowedBounds, getMinimalMedium, and others);
  parseGrRule, grRuleToString, getGenesFromGrRules and getAllRxnsFromGenes
  are covered by cobrapy's own GPR/Gene classes, not previously recorded
  anywhere.

• 38 are deliberately absent, each with its own reason: internal helpers
  already folded into an already-mapped public function (buildEquation,
  constructS, parseRxnEqu, the three KEGG global-model builders, the sample*
  rounding/warmup subroutines, writeExcel, cleanSheet), MATLAB-specific
  plumbing with no Python equivalent needed (parseRAVENargs, printOrange,
  ravenList, the two notice/warning helpers, parallelWorkersRAVEN,
  setRavenProgress, checkFileExistence, the two MATLAB-struct-field-order
  functions and their registry, runRAVENtests), and a handful
  raven-toolbox genuinely has no equivalent for yet (findPotentialErrors,
  getTransportRxns, removeBadRxns, reverseRxns, readFasta,
  runRobustnessAnalysis, runSimpleOptKnock), confirmed by grepping the
  raven-toolbox source rather than assumed absent.

• docs/raven3-migration.md: at over 500 lines, this page mixed an orientation
  checklist with twelve detail sections. Kept the checklist and an
  "if you read nothing else" box on the landing page, moved the rest into
  four grouped pages under docs/raven3-migration/: what moved/was
  removed/was renamed, the full backward-incompatible punch list, file
  formats and reconstruction pipelines, and new functionality plus
  dependencies and error handling. Every section cross-reference, including
  the ones from docs/guide/io.md and docs/tutorials/index.md into specific
  sections, now points at the page the content actually moved to.

• docs/raven3-vs-raven-toolbox.md: same problem at a smaller scale. Kept the
  orientation content (which one to use, naming, solvers) on the landing
  page, moved "what each has" and "same function, different answer" into
  docs/raven3-vs-raven-toolbox/. Retitled from "RAVEN and raven-toolbox" to
  "RAVEN vs. raven-toolbox".

• docs/installation/raven.md: none of the three install methods actually
  installs the 3.0.0b1 pre-release this site documents. The Add-Ons manager
  and the GitHub releases page both only ever offer the latest stable
  release (RAVEN 2.x); a plain git clone tracks main, also RAVEN 2.x.
  Added a warning and pointed at what actually works: a direct archive
  download of the 3.0.0b1 tag, and git clone plus an explicit checkout of
  that tag. Fixed the Upgrade tab's git pull origin main the same way; a tag
  doesn't move, so upgrading past it means switching to the develop3
  branch, not pulling the tag.

• docs/yaml-format.md: moved from under Parameter tuning to a new "Start"
  section under Guide (renamed from "Installation", now installation plus
  this page), and retitled from "RAVEN / cobrapy YAML model format" to
  "YAML file format".

• docs/index.md: bolded "MATLAB" and "Python" in the tagline; split the
  MATLAB (Add-Ons) tab's two instructions onto separate lines, they were
  running together as one sentence.

• docs/conf.py: the navbar had one GitHub icon, linking to the MATLAB repo
  only; added a second, linking to raven-toolbox.