Docs: terminology drift, overloaded 'Layer' term, stale figures, and misc glitches

[codeforester]

Goal

Fix a cluster of smaller consistency and polish issues: interchangeable
terminology for the same concept, an overloaded "Layer" term, stale
maintainability figures, redundant "what Base is not" lists, and a few
concrete doc glitches.

Background

A documentation review surfaced several smaller but real issues that don't
warrant their own tracking issue individually but are worth fixing together:

• Terminology drift: "repo set" (README.md:13,27,1887,1894,1959;
  docs/why-base.md:9), "repository set" (README.md:750; FAQ.md:370),
  hyphenated "repo-set" (docs/why-base.md:47,77), and "repo family"
  (README.md:754) are all used interchangeably for the same concept with no
  glossary entry tying them together.
• Overloaded "Layer" term: docs/architecture.md:47-58 (numbered 1-4
  "Product Responsibility Layers") and :196-254 (numbered 1-3 "Shell
  Environment Layers") both start at "Layer 1" in the same document, and
  docs/technical-overview.md:69 ("Architecture: Three Layers") only mirrors
  the second sense — a reader has no way to know which "Layer 1" is meant on
  a skim.
• Redundant "what Base is not" lists: four separately-worded renderings
  of essentially the same list exist — docs/tool-boundaries.md:45-54 and
  :748-760 (near-verbatim within the same document, ~700 lines apart, and
  already worded slightly differently), docs/product-requirements.md:218-235
  ("Non-Goals"), and docs/architecture.md:819-833 ("What Base Is Not") —
  none marked as the canonical version.
• Stale maintainability figures: docs/product-assessment.md:296-299
  cites line counts (repo.sh ~3,400, setup_common.sh ~2,170, repo.bats
  ~1,730, gh.bats ~1,000) that no longer match the codebase — actual
  repo.bats is 3,190 lines, setup_common.sh is 1,521, gh.bats is 1,679.
• Repeated near-verbatim note: "Ubuntu/Debian support from Implement first supported Linux runtime target #562 has since
  shipped" (or an equivalent restatement) appears near-verbatim across at
  least four dated entries in docs/product-assessment.md
  (:216-218,281-282,342-343,394-396,437-439) instead of being consolidated
  once.
• Concrete glitches: docs/cache-ownership-and-layout.md:58's ASCII
  directory-tree diagram has a misaligned │ connector (4 spaces where a
  continuation bar is needed, given base/ is not the last root entry);
  docs/basectl-onboard.md:36-45 vs :120-130 prints the same options table
  twice with the --yes description differing slightly between copies; and
  docs/doctor-findings.md:121 (BASE-D011) vs :130 (BASE-D105) are two
  differently-scoped findings with near-identical names, despite the doc's
  own recommendation (line 6) that automation match on (id, name).

Scope

• README.md, docs/why-base.md, FAQ.md (terminology only)
• docs/architecture.md, docs/technical-overview.md ("Layer" terminology)
• docs/tool-boundaries.md, docs/product-requirements.md,
  docs/architecture.md ("what Base is not" consolidation)
• docs/product-assessment.md (stale figures + repeated note)
• docs/cache-ownership-and-layout.md, docs/basectl-onboard.md,
  docs/doctor-findings.md (concrete glitches)

Acceptance Criteria

• One term is picked for "a set of independently-checked-out
  repositories" and used consistently, or the doc set explicitly notes
  the synonyms in a glossary entry.
• docs/architecture.md disambiguates its two "Layer" taxonomies (e.g.
  distinct names, or explicit "not to be confused with" note).
• The "what Base is not" content exists in one canonical place with the
  others linking to it, and the two copies within tool-boundaries.md
  are merged into one.
• product-assessment.md's maintainability figures are refreshed to
  current line counts (or replaced with a note pointing to a
  live-computed source instead of hardcoded numbers).
• The repeated Ubuntu/Debian-shipped note in product-assessment.md is
  consolidated to a single statement.
• The ASCII tree in cache-ownership-and-layout.md, the duplicate table
  in basectl-onboard.md, and the finding-name collision in
  doctor-findings.md are each fixed.

Validation

git diff --check; for the ASCII tree and duplicate table, visually confirm
the rendered markdown looks correct.

Non-Goals

• Introducing a formal glossary document (a simple consistent word choice is
  enough unless the maintainer wants a glossary as a separate effort).

Project Metadata

• Priority: P3
• Size: M
• Area: Docs
• Initiative: Adoption Polish
• Agent Assignment: Copilot candidate after triage (mostly mechanical
  find/replace and figure updates, with a few small editorial merges)