Introduces a new LAIType = 2 path for vegetation phenology and threads
the plumbing end-to-end without changing numerical behaviour. The new
branch mirrors LAIType = 0 exactly (bit-identical on the sample run);
the Design C Jarvis + CLM5-persistence-trigger numerics land in PR2.

Fortran physics
  - LAI_PRM gains six moisture parameters (w_wilt, w_opt, f_shape,
    w_on, w_off, tau_w). Thresholds operate on dimensionless relative
    soil water w = 1 - smd/smdcap; tau_w is in days.
  - PHENOLOGY_STATE gains three per-veg-surface slots (wbar_id,
    w_id_prev, leaf_on_permitted).
  - update_GDDLAI signature extended with previous-day SMD (mm), SMD
    capacity (mm), the six moisture parameters and the three state
    arrays. LAIType == 2 branch is a no-op with TODO(PR2) markers;
    the LAI power-law now explicitly routes LAIType == 2 through the
    original (LAIType == 0) curve so scaffolding is bit-identical.

Rust/C bridge (schema v1 -> v2)
  - LAI_PRM flat length 11 -> 17 in lai.rs and c_api/lai.f95.
  - PHENOLOGY_STATE flat length 76 -> 85 in phenology.rs,
    c_api/phenology.f95, and c_api/driver.f95:104 aggregate; driver.f95
    pack_phenology_state extended for the three new arrays.
  - Embedded LAI slices widen LC_DECTR_PRM 61 -> 67, LC_EVETR_PRM
    57 -> 63, LC_GRASS_PRM 55 -> 61; shadow types, pack/unpack, and
    Rust slice offsets updated on both sides.
  - yaml_config.rs honours the six new lai.* keys when overriding.

Python data model
  - LAIParams exposes six optional FlexibleRefValue(float) fields and a
    laitype=2-only validator that checks w_opt > w_wilt and
    w_off < w_on and logs unset moisture fields.
  - to_df_state / from_df_state serialise the new columns with safe
    defaults so legacy YAMLs keep loading.
  - checker_rules_indiv.json adds six grid-level entries so run_supy's
    check_state() does not reject the new df_state columns.

Tests and diagnostics
  - test/data_model/test_laiparams_moisture_fields.py: four tests
    covering default load, explicit round-trip, validator scoping, and
    checker-rule coverage.
  - test/test_phenology_lai_type_scaffolding.py: bit-identity of
    LAIType = 2 vs LAIType = 0 on the bundled sample (the sample
    defaults to laitype=1, so the test mutates the initial state
    explicitly), plus a no-NaN sanity run for laitype=1.
  - scripts/verify/moisture_phenology_site.py: standalone diagnostic
    harness for the eventual FLUXNET2015 comparison (AU-ASM by
    default); reads from the local FLUXNET archive, caches under
    .context/gh1292/<site>/, emits lai_timeseries.png, metrics.json
    and summary.txt. Informational in PR1 (V0 == V2); becomes the
    scientific acceptance harness in PR2.

Design record
  - dev-ref/design-notes/gh1292-moisture-phenology.md (from commit
    2a019ba) captures the full design; this PR implements the PR1
    slice described there.

…oisture

# Conflicts:
#	CHANGELOG.md

…oisture

Replaces the PR1 no-op in update_GDDLAI LAItype=2 branch with the
Design C hybrid scheme from the internal design note: a Jarvis-style
water-stress factor on delta_GDD plus a CLM5-style persistence latch
on the tau_w-day running mean of relative soil water.

Fortran physics
  - Jarvis f_w: f_w = 0 when w <= w_wilt, f_w = 1 when w >= w_opt, and
    a piecewise-power curve on the intermediate interval.
  - CLM5 latch: leaf_on_permitted flips off when wbar_id drops below
    w_off and flips back on when wbar_id rises above w_on while the
    thermal companion delta_GDD > 0 is satisfied. When the latch is
    closed, delta_GDD is zeroed out.
  - Seed wbar_id from the first measured w (detected when w_id_prev
    and wbar_id are both still at their zero defaults) so well-watered
    sites do not spend tau_w days ramping up from zero.
  - PHENOLOGY_STATE.leaf_on_permitted default flipped from false to
    true across Fortran, Rust bridge, and C shadow so mid-year starts
    and wet-site configurations do not wait for the persistence
    trigger before accumulating GDD.

Tests
  - test_phenology_lai_type_scaffolding.py rewritten for PR2
    semantics: bit-identity now holds in the well-watered regime
    (default thresholds on the Swindon sample), aggressive Jarvis
    thresholds strictly reduce mean LAI, and depleting soilstore_surf
    to 10 mm on day 1 demonstrably delays spring green-up over the
    first 60 days.
  - Legacy laitype=1 sanity check preserved.

CHANGELOG entry added; Rust bridge unit tests (lai, phenology) still
pass after the default flip.

Introduces a parameter-sweep tool, documents the calibration
methodology, and runs a sensitivity demo on the bundled Swindon
sample. Does not attempt a full per-IGBP FLUXNET fit (that requires
dedicated per-site SUEWS configurations outside this repo) and does
not add the optional additive moisture-stress SDD term (deferred
until calibration data motivates it).

scripts/verify/moisture_phenology_sweep.py
  - Scans one of the six moisture parameters (w_wilt, w_opt, f_shape,
    w_on, w_off, tau_w) over user-supplied or default value lists,
    reruns SUEWS per value, reports mean LAI, RMSE vs LAIType=0
    baseline, seasonal amplitude, green-up DOY, and emits a dual-axis
    sensitivity PNG alongside the JSON payload.
  - --all flag scans all six parameters sequentially.
  - --dry-start depletes vegetation soilstore_surf to 10 mm on day 1
    so the moisture gate engages at otherwise well-watered samples
    (Swindon sample is UK-suburban).
  - Pairwise-validator co-adjustment keeps w_opt > w_wilt and
    w_on > w_off satisfied during extreme sweep values.
  - Outputs land in .context/gh1292/<site>/sweep_<param>.{json,png}.

dev-ref/design-notes/gh1292-moisture-phenology.md
  - New Appendix A covering: sweep-tool usage (A.1); Swindon
    sensitivity results and the "w_wilt, w_opt, w_off" sensitive-trio
    finding (A.2); FLUXNET2015 calibration roadmap with primary
    dryland/monsoon tier and temperate control tier and acceptance
    bars from section 8 (A.3); status of the optional SDD
    senescence term as deferred (A.4).

test/test_moisture_phenology_sweep.py
  - Slow-tagged CLI smoke test that runs a one-point sweep and
    validates the JSON schema (parameter name, baseline mean LAI,
    five required fields per point).

CHANGELOG entry added for 18 Apr.

Introduces a lightweight system for archiving dashboards and narratives
that accompany scientific PRs:

- New `docs/source/development/` tree exposed via the main toctree, with
  a landing page explaining the dev-notes convention.
- Sphinx `html_extra_path` now includes `docs/source/_extra/`, so per-PR
  dashboards placed under `_extra/dev-notes/<slug>/` are copied verbatim
  into the built site at `/dev-notes/<slug>/`.
- `scripts/suews/build_dev_note.py` classifies assets as light (copied
  in-repo) or heavy (staged for a GitHub Release tagged
  `dev-notes-<slug>`), rewrites heavy-asset URLs in the source
  dashboard, and emits the release commands for the operator.

- Adds `.github/pull_request_template.md` with a check-box classifier
  (Bug / Refactor / Docs / Tooling / Scientific) and a scientific-PR
  sub-checklist that asks for tests, a dev-note dashboard, and the
  associated `docs/source/development/<slug>.rst` narrative.
- Extends the audit-pr skill with a dedicated Step 3 "Scientific PR
  dev-note demo" block mirroring the template: reviewers verify that
  scientific PRs ship with a runnable dashboard under
  `docs/source/_extra/dev-notes/<slug>/` and a summary page in
  `docs/source/development/`, and that the dev-notes toctree has been
  updated.

Fills the newly introduced dev-notes slot for the moisture-aware LAI
phenology work:

- New dashboard + narrative
    - `docs/source/development/gh-1292-lai-moisture.rst` summarises the
      problem, Design C mechanism, three-PR landing, and links to the
      full internal design note.
    - `docs/source/_extra/dev-notes/gh-1292-lai-moisture/dashboard.html`
      is the self-contained demo (hero metrics, four-panel drought
      demo, Design C equations, sensitivity summary, commit timeline).
- Two publication-quality demo figures with a unified panel-label
  convention — left edge aligned with the y-axis-label column, two
  scenarios (solo letter vs labelled title) sharing one helper:
    - `scripts/verify/moisture_phenology_drought_demo.py` — 4-panel
      London drought scenario showing the two control branches; solo
      `A)`/`B)`/`C)`/`D)` labels.
    - `scripts/verify/moisture_phenology_sensitivity_summary.py` —
      two-panel sensitivity ranking + dose-response; labelled-title
      `A)`/`B)` that concatenate the panel description.
- `moisture_phenology_sweep.py` and the two tests now default to the
  London sample (Ward et al. 2016 KCL benchmark); the bundled sample
  config was never Swindon.
- Design-note Appendix A updated with the same London-vs-Swindon fix
  and the sensitivity-trio finding (`w_wilt`, `w_opt`, `w_off`).
- CHANGELOG entries for PR2 and PR3 rewrite "Swindon" → "London" for
  the same reason.

Rolls back 3a272c8 and the GH-1292 dashboard artefacts from 5991fb4.
Keeps the scientific substance (verify scripts, tests, CHANGELOG,
design note) but drops the archival layer — evidence for scientific
PRs lives in GitHub PR comments and linked verify scripts + figures,
not in a parallel RST/dashboard pipeline.

…ecklist"

Rolls back 9583f47. Scientific PRs do not need a dedicated review
track or a dashboard-delivery requirement — ordinary PR description,
review, and comments are the right venue for evidence and discussion.
Drops the PR template along with the audit-pr Step 3 dev-note section.

The previous PR2 code used 0.0 as the "unset" marker for `wbar_id` and
`w_id_prev` on first activation, but 0.0 is a physically valid value of
dimensionless relative soil water (completely dry). A site that began a
timestep with `w = 0` would wrongly be re-seeded every step instead of
advancing the running mean.

Switch the unset sentinel to -1.0 (outside the physical [0, 1] range
that `w` is clamped to) and check `< 0.0` in `update_GDDLAI`. Applies
consistently across:

- `PHENOLOGY_STATE%wbar_id`, `%w_id_prev` in `suews_type_vegetation.f95`
- `update_GDDLAI` seed-detection in `suews_phys_dailystate.f95`
- The `phenology_state_shadow` defaults in the Rust/C bridge
  (`suews_bridge/c_api/phenology.f95` + `suews_bridge/src/phenology.rs`)

Rewrites `scripts/verify/moisture_phenology_site.py` so the forcing is
parsed via SuPy's `read_forcing()` utility (preserving subhourly
minute resolution instead of the ad-hoc Y%j%H reconstruction), and so
`run_scenario()` takes the forcing and run window as explicit
arguments rather than silently picking them up from the sample config.

Adds `test/test_moisture_phenology_site.py` covering:
- `load_forcing()` preserves 30-min timestamps and filters by year
  correctly using the new SuPy parser
- `run_scenario()` threads the caller-supplied forcing and date window
  through to SuPy rather than swallowing them

…oisture

# Conflicts:
#	CHANGELOG.md