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Integrate depth-dependent soil extraction and optional multi-year spin-up - #9
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The latest soil-extraction physics and multi-year initialization were available on separate branches. Integrate both into main so the daily v3 depth-dependent extraction formulation applies to ordinary runs and explicitly enabled repeated spin-up.
Root extraction uses the depth-dependent GSSM/WP threshold while preserving continuous three-day relaxation and physical zero-to-porosity bounds. Repeated calendar-block spin-up retains leap days, uses bounded memory, reports convergence diagnostics, and remains disabled unless explicitly enabled. Existing v2 fitted coefficients require recalibration; immutable reference artifacts remain compatible. Documentation and integration coverage include enabled and disabled initialization.
Validation: all 183 tracked files exactly match the frozen combined source from commit 70b0e8c (tree ef89dc8cead067099803a01e66e9cb802e138917). That source passed all 515 tests with zero failures or skips in Gadi PBS job 181813704 (exit 0). The integration records both published feature branches as ancestors and retains the combined-physics/spin-up regression test. Git whitespace checks pass. GitHub matrix tests, builds, and installed-wheel demos must pass before merge.