Add unit tests for v0.40.0 surface (lnk_mapping_code, persist additions, pipeline_run mapping_code phase, deprecation shims)

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Context

v0.40.0 (#187) landed substantial new R code without dedicated unit tests. Compile-time checks + /code-check rounds caught real bugs during implementation (Phase 2's conditional-col dropouts, Phase 4's missing roxygen, Phase 6's body-ref renames after signature rename), and the existing 1119-test suite continued to pass — but no new test files / test_that blocks were added for the new surface.

Coverage gaps

Surface	Current state	Gap
R/lnk_mapping_code.R (new exported function)	no test file	tests/testthat/test-lnk_mapping_code.R missing entirely
R/lnk_persist_init.R — new cols_streams_access_base / cols_streams_mapping_code_base + per-species helpers + CREATE TABLE / VIEW blocks	existing 10 tests cover the pre-#187 schema	no test asserts the new tables/view exist post-init, no test asserts per-species column naming
R/lnk_pipeline_persist.R — new streams_access + streams_mapping_code write blocks (gated on working-table presence)	existing 6 tests cover pre-#187 writes	no test asserts the gated-write logic (skip when working table absent; fire + JOIN-back when present)
R/lnk_pipeline_run.R — new mapping_code = FALSE param + conditional phase	existing 8 tests cover pre-#187 flow	no test asserts the new phase fires + writes expected tables when mapping_code = TRUE
R/lnk_pipeline_mapping_code.R — species_<role> param rename + deprecation shims	existing tests use old param names	no test asserts the deprecation shim warns + remaps correctly

Goals

Add the missing tests with mocks (same with_mocked_bindings pattern as test-lnk_compare_wsg.R) so:

• tests/testthat/test-lnk_mapping_code.R — covers query construction (table_* args), habitat long→wide pivot, presence derivation logic, species_<role> pass-through to lnk_pipeline_mapping_code, error paths (empty access, empty habitat).
• test-lnk_persist_init.R extended — assert <schema>.streams_access, <schema>.streams_mapping_code, and <schema>.streams_habitat_long_vw exist after init with the species-driven column set. Assert per-species column naming convention.
• test-lnk_pipeline_persist.R extended — assert new write blocks skip cleanly when working tables absent (gating); assert they fire with correct JOIN projection when present.
• test-lnk_pipeline_run.R extended — assert mapping_code = TRUE triggers the new phase (mock lnk_barriers_views + lnk_pipeline_access + lnk_mapping_code and verify call ordering); assert mapping_code = FALSE (default) does not.
• test-lnk_pipeline_mapping_code.R extended — assert deprecation shims for resident_species / anadromous_species / spawn_only_species emit .Deprecated() warning and remap to species_<role>.

Acceptance

• devtools::test() count increases by 15–25 test_that blocks across the five files (rough estimate based on the surface size).
• All new tests use mocks; none require a live DB.
• Deprecation-shim tests verify both warn-on-use and functional-remap.
• 0 FAIL throughout.

References

• R/lnk_mapping_code.R — new function, no test file.
• R/lnk_persist_init.R lines 60–115 (new cols + helpers) + 232–263 (new CREATE TABLE / VIEW).
• R/lnk_pipeline_persist.R lines 104–172 (new write blocks).
• R/lnk_pipeline_run.R lines 138–190 (new mapping_code phase).
• R/lnk_pipeline_mapping_code.R lines 95–122 (deprecation shims).
• Follows from mapping_code build decoupled from tunnel — persist streams_access + lnk_pipeline_run phase + rename with_mapping_code → mapping_code #187 — landed without these tests; this issue tracks the catch-up.