docs: clarify terminology and boundaries

[codeforester]

Summary

• standardize the documentation term to repository set and disambiguate product responsibility tiers from shell environment layers
• consolidate the canonical Base non-goals in docs/tool-boundaries.md and link the architecture and requirements references to it
• replace stale maintainability counts with a live wc -l command and consolidate repeated Ubuntu/Debian notes into the current platform contract
• fix the cache tree connector, duplicate onboard options table, and doctor finding-name collision

Why

These were small but user-facing documentation inconsistencies: readers could encounter different names for the same repository concept, two unrelated Layer 1 taxonomies, duplicated boundary lists, stale measurements, or conflicting option/finding descriptions.

Validation

• git diff --check
• /Users/rameshhp/.base.d/base/.venv/bin/pytest tests/test_base_cli_docs.py tests/test_docs_version.py tests/test_doctor_findings_docs.py tests/test_setup_common_ownership_docs.py tests/test_contract_hardening.py tests/test_linux_support_docs.py -q (26 passed)
• manually inspected the corrected ASCII tree, canonical onboard options block, and finding table

Issue

Fixes #1950