Docs: config-precedence and environment-variable reference docs disagree with each other

[codeforester]

Goal

Reconcile the config-precedence and environment-variable reference docs,
which currently disagree with each other on layer count and which variables
exist.

Background

A documentation review of the reference/contract layer found:

• Config precedence order is documented twice with different layer counts
  and different treatment of --config's position relative to env vars/CLI
  options: docs/local-config.md:89-100 (5 layers) vs.
  docs/base-cli.md:301-310 (6 layers), with no cross-reference between the
  two "contract" pages.
• docs/local-config.md:102-106's "Recognized environment variables" list
  (3 vars) omits BASE_CLI_TEMP_RETENTION_DAYS, which docs/base-cli.md's
  Standard Environment Variables table (:328-335) and
  docs/runtime-environment.md:206 both include as part of the same config
  layer.
• docs/python-manifest.md:66 references BASE_PROJECT_PYTHON_BIN as an
  interpreter-selection input, but it is completely absent from
  docs/runtime-environment.md, which bills itself (line 6) as "the
  canonical reference for Base-managed shell environment variables" and
  documents closely related knobs like BASE_PROJECT_VENV_DIR.
• docs/workspace-manifest.md:490-493 and docs/python-manifest.md:304-309
  describe the same python_runtime JSON field for workspace status --format json almost verbatim, with no cross-link between the two.

Scope

• docs/local-config.md
• docs/base-cli.md
• docs/runtime-environment.md
• docs/python-manifest.md
• docs/workspace-manifest.md

Acceptance Criteria

• Config precedence order is stated once, correctly, and the other doc
  cross-references it instead of restating a (possibly different) count.
• docs/local-config.md's recognized environment variables list matches
  docs/base-cli.md/docs/runtime-environment.md exactly, or explains
  why it's a deliberate subset.
• BASE_PROJECT_PYTHON_BIN is documented in
  docs/runtime-environment.md (or the doc explains why it's out of
  scope there).
• The duplicated python_runtime field description is consolidated into
  one canonical location with a cross-reference from the other.

Validation

git diff --check; if feasible, verify actual config-resolution order
against the CLI's implementation to confirm which layer count (5 or 6) is
correct before documenting it.

Non-Goals

• Changing actual config-resolution behavior — this is a documentation
  accuracy/consolidation issue.

Project Metadata

• Priority: P1
• Size: M
• Area: Docs
• Initiative: Contract Hardening
• Agent Assignment: Human first (need to verify actual precedence behavior
  against the codebase before picking which doc is correct)