@woosh/meep-engine 3.60.4 → 3.60.6

package/src/generation/foliage/SELF_ORGANIZING_FRAMEWORK_BRIEF_2026_10_26.md

@@ -1,347 +0,0 @@
-# A Framework Grown from Shoots
-
-Alex, 2026-10-26: grow the framework from the same shoot demography and light as the twigs (self-organizing), keeping
-the generator graph only for what shoots cannot give. Brief first.
-
-Why: `CROWN_FULLNESS_BRIEF_2026_10_26.md`. The crowns are bare because the authored framework is sparse
-(`BranchSpawnRule.count`). Vigour does not fill them; doubling the counts does. Every bare preset carries a third to
-two-thirds of the leaf a real tree of its size does.
-
-## Today
-
-1. **`tree_skeleton_grow`** builds the framework from the generator graph. `branches[0]` is the trunk, and each
-   `branch_rules` edge spawns `count` branches of one generator along another. The generator graph supplies:
-   - Hermite spines with tropisms (gravitropism, phototropism, plagiotropism, straightness, curl-noise gnarl, nodal
-     kinks);
-   - phyllotaxis, whorls, splits, space colonization toward an authored crown envelope, and BVH avoidance;
-   - dead stubs and scars (`self_pruning`), surface roots, flare lobes;
-   - pipe-model radii.
-2. **`tree_skeleton_grow_shoots`** then grows the twig layer on the finished framework, season by season. The work is
-   done by `shoot_systems_simulate`: a light field, net yield by light, shedding, dynamic girth (`ShootGirth`),
-   collision against the framework, and engulfment. A carrier's age is backed out of its position.
-
-The framework's density, its bough count, its envelope and its age are all authored or backed out. Only the
-periphery is grown.
-
-## Principle
-
-A tree is its shoots. From the seedling on, each season every living axis extends and its buds burst by the
-species' bud demography. Each new shoot is kept as its light pays for it, and the wood thickens with what it carries.
-- **The framework** is the shoots that survived.
-- **Bough spacing** is what self-shading leaves.
-- **The crown's extent** is where the leaders reached in the tree's age.
-- **Natural pruning** is the lower boughs starving.
-
-This is the self-organizing tree of Palubicki et al. (2009, *ACM Trans. Graph.* 28(3): 58): bud fate by local light
-and space, and growth year by year. LIGNUM (Perttunen et al. 1996, *Ann. Bot.* 77: 87-98) grows a whole tree from
-annual units the same way. The simulation already is this, for the periphery; extending it to the whole tree is the
-change.
-
-**What shoots cannot give**, so the generator graph keeps it:
-- **The root system:** surface roots and the flare lobes. These are not shoot growth.
-- **Monocots:** the palm and the fern grow fronds from one apical meristem, with no lateral shoot system. Their
-  presets stay on the graph entirely.
-- **The seed:** the seedling's first leader, its position, and the trunk guide as an initial direction.
-
-## Design
-
-1. **One simulation from the seedling.**
-   - `tree_skeleton_grow` lays the roots and a seed leader.
-   - `shoot_systems_simulate` grows everything else for the tree's `age` seasons: the leader is an order-1 axis, the
-     boughs are its laterals, and so on down the orders. Each preset's `shoot_rules` cover every order from the stem
-     out, not only the periphery.
-   - Carriers, "framework age" and `branch_unit_start_t`'s carrier back-fill go away: every axis records its own units
-     as it grows them.
-2. **The light field grows with the crown.** The voxel grid follows the crown's bounds each season, not a fixed
-   framework box, at the same cell. Cost is still grid cells times 17 sweeps.
-3. **Shoots keep out of all older wood.** Each shoot is tested against wood as thick as it is that season.
-   - That replaces the BVH avoidance and the framework hash: one spatial hash over every living segment, updated
-     incrementally, since each season only adds units and thickens wood.
-   - Engulfment stays: wood that thickening wood grows into dies.
-4. **Natural pruning is shade death.**
-   - A whole bough dies when its shoots cannot pay for themselves (`Rb < 1` everywhere on it). Today that holds for
-     twig axes only.
-   - Its dead wood persists as a stub by the species' `self_pruning`, as the graph's stubs do now, then heals over
-     into a scar (`TreeSkeleton.add_scar`).
-   - The graph's stub and scar code moves to the simulation, driven by deaths rather than an authored `attach_min`.
-5. **Tropisms per axis order.**
-   - The shoot simulation already turns each new unit by its generator's gravitropism, phototropism and zigzag.
-     Plagiotropism and straightness move over from the graph's spine to the unit's heading.
-   - Older wood does not move once grown, except by bending (fork F3).
-6. **Architecture stays sourced data.**
-   - **Excurrent conifers:** a leader whose terminal is longest and whose whorl buds burst every year.
-   - **Sympodial birch:** the apex aborts and the subapical buds take over, already in the rule.
-   - **Decurrent oak:** the order lengths fall with order.
-   - These are the rules' per-order lengths and bud zones. No apical-control constant is added unless a measurement
-     shows the forms do not come out (fork F4).
-7. **The bark mesher, the wind rig and the foliage** keep reading the skeleton as they do. Every branch is now a
-   chain of annual units: more nodes on old boughs, one a year.
-
-## Data per species
-
-What the rules need from the stem out, and what the presets already cite:
-
-| preset | stem and boughs | gap |
-| :--- | :--- | :--- |
-| pine | leader 47.5 cm/yr and shoot counts by branch order [Kellomäki & Kurttio 1991] | the leader rule bears no laterals today; the stem's whorl bud counts are to be found, in KK1991 or elsewhere |
-| spruce | Colin & Houllier 1992 (whorl and interwhorl branches); lengths by order from pine | leader growth borrowed from pine |
-| birch | stem long shoot 26.3 cm [Lintunen et al. 2011, Table A2]; Maillette 1982 orders | stem bud zones as the branches' |
-| maple | stem is Wilson's order 1, leader 30 cm/yr [Wilson 1966; Critchfield 1971] | none known |
-| willow | Remphrey & Pearn 2006 orders | stem rule |
-| oak | Buck-Sorlin & Bell 2000 cover mature crowns' peripheral branches, not the stem or boughs; leader 0.3 m/yr is chosen | a source for oak's leader and bough demography (sapling architecture studies) |
-| hazel | a stool: basal sprouts from the root collar [Grisafi et al. 2024 for the shoots] | the stool's sprout recruitment |
-
-**Targets (acceptance):**
-- whole-tree leaf area within the allometric range at the tree's DBH (`CROWN_FULLNESS_BRIEF`, Forrester et al. 2017,
-  Martin et al. 1998, Repola 2009);
-- FIA crown density 45-51% with transparency near 15% [Randolph 2006];
-- a height-to-diameter ratio in the measured range for the species.
-
-## Decisions (Alex, 2026-10-26)
-
-- **F1:** from the seedling, for the tree's age.
-- **F2:** sapwood carries the leaf: girth from the species' leaf-to-sapwood ratio, with heartwood inside.
-- **F3:** static sag from the beam mechanics.
-- **F4:** no apical control until a measurement asks for it (as recommended; not asked).
-- **F5:** research a *Quercus* stem and bough source; oak keeps its graph framework until then.
-
-## Forks
-
-- **F1 Time.** Simulate from the seedling for the tree's age, or start from a sapling.
-  - Recommended: **from the seedling**. The size then follows from the leader growth and the age, and nothing is
-    backed out.
-  - The preset's input becomes `age` (seasons).
-- **F2 Wood.** The pipe model at `pipe_model_exponent` over Table 7 shoot radii gives an 87 cm DBH oak 8.6 m tall.
-  - Recommended: **sapwood carries the leaf** (Shinozaki et al. 1964). A cross-section's sapwood area is the leaf
-    area it carries over the species' measured leaf-to-sapwood ratio (Norway spruce 0.45 m²/cm², Pokorný & Tomášková
-    2007; red maple and oaks from Martin et al. 1998), and heartwood accrues inside it.
-  - The ratio is sourced, and the DBH then follows from the leaf. It lands in the same pass (`ShootGirth`).
-- **F3 Bending.** Old boughs droop under their own weight; graph spines fake it with authored curvature.
-  - Recommended: **static sag from the existing beam mechanics.** The segment compliance and loads are already
-    computed for the wind joints, so the deflection under self-weight comes from them, applied once per season as the
-    wood grows.
-  - Alternatively, defer, and tropisms alone shape the boughs.
-- **F4 Apical control.** Recommended: none beyond the rules' order lengths at first, then measured. Add a sourced
-  control only if the excurrent and decurrent forms do not emerge.
-- **F5 Oak's stem data.** Recommended: research a sapling or young-tree architecture source for *Quercus* before oak
-  migrates. Until then, oak keeps its graph framework and the brief says so.
-
-## Plan
-
-1. **S0, the gate.** A probe and spec that measure every preset against the targets: leaf area vs allometry, FIA
-   density and transparency, H/D, crown width/height. Run on master as the baseline.
-2. **S1, pine end to end.**
-   - The seed leader plus the whole-tree simulation (light field following the crown, collision against all wood,
-     shade death of boughs). Roots stay on the graph.
-   - Pine first: the best data from the stem out.
-   - Measure against S0; look at it.
-3. **S2, wood from leaf** (F2): sapwood by the leaf-to-sapwood ratio, heartwood, and the H/D check.
-4. **S3, stubs and scars from deaths**, moved off the graph.
-5. **S4, bending** (F3), if taken.
-6. **S5, the other species:** spruce, maple, birch, willow, hazel, then oak once F5 has a source. Each is measured
-   against S0 and looked at.
-7. **S6, removal.** Struck 2026-10-28: the generator graph is a front end of its own (TWO_FRONT_ENDS_BRIEF_2026_10_28.md,
-   G-F7), so its crown machinery stays.
-   - The graph's crown machinery goes for shoot-grown species (hard break): branch spawn rules above the roots, space
-     colonization, the crown envelope's growth role, BVH avoidance, and the back-filled carrier ages.
-   - Specs are restated from their principle. Tiers come from whorls; collision is "a shoot never grows into older
-     wood".
-   - Mutation-tested.
-
-## Risks, to measure, not assume
-
-- **Cost.** The whole tree as shoots means more axes and seasons. Today spruce is 3.1 s with 40k twig axes. Measure at
-  S1, then decide whether the light field or the hash needs work. There is no preset budget.
-- **Mesh size.** Old boughs get a node a year. Measure node and triangle counts at S1 against today's.
-- **Specs.** Most framework specs restate (tiers, collisions, stubs, seams); the root and monocot specs stand.
-- **The trunk's look.** Flare lobes and bark keep working on any trunk. The trunk guide becomes the seed leader's
-  initial heading plus tropisms.
-
-## S0 baseline (seed 1337, master 7d610267e)
-
-`analysis/tree_leaf_area_targets.js` holds the sourced allometries; the gate probe compares each preset to them at the
-tree's own DBH and height, and reports the DBH a measured tree carrying the preset's leaf would have.
-
-| preset | DBH | height | H/D | leaf | expected at its DBH | leaf implies DBH | side density | transparency |
-| :--- | ---: | ---: | ---: | ---: | ---: | ---: | ---: | ---: |
-| oak | 87 cm | 8.6 m | 10 | 89 m² | 1,347-2,297 m² (outside every sample) | 19 cm | 0.50 | 0.42 |
-| pine | 73 cm | 10.7 m | 15 | 16 m² | 168-245 m² (outside every sample) | 16 cm | 0.34 | 0.64 |
-| birch | 62 cm | 10.5 m | 17 | 70 m² | 582 m² (outside the sample) | 20 cm | 0.56 | 0.33 |
-| maple | 88 cm | 8.6 m | 10 | 51 m² | 899 m² (outside the sample) | 17 cm | 0.41 | 0.42 |
-| spruce | 69 cm | 10.8 m | 16 | 78 m² | 482-730 m² | 21 cm | 0.33 | 0.31 |
-
-Every tree fails the leaf gate by 6-16x at its own DBH, because both halves are off: the trunks are three to four
-times too thick (S2), and the crowns carry a third to two-thirds of the leaf of a tree as tall (S1). Willow, palm,
-shrub and fern have no allometry. Only oak and fern sit in the FIA density band; no preset is near 15% transparency.
-
-## S1 status (2026-10-26, uncommitted)
-
-**Built:**
-- **The stem from the seed.** The graph lays a seed leader (the first year's shoot) and the roots. A carrier that
-  stops growing before the tree's `ShootGrowthConfig.age` grows on from its tip as an axis of its own order and
-  generator, and is written onto the carrier, so the trunk is one branch from the ground up.
-- **The leader by height.** The stem grows `leader_unit(height)` a year: KK1991 Eq. 6's logistic. KK1991 grow the
-  stem this way because the stem's terminal ratio (1.196) has no bound.
-- **Per-order demography.** `ShootSystemRule.target` is a generator per mother order (the stem's laterals draw the
-  bough generator, the rest twigs); `mean_unit_length` is per order; a new shoot survives at Rb over the gross yield of
-  the unit it grew on, counted at that unit's own length.
-- **Light, ground, crown frame.** The light field is rebuilt round the crown as it grows; no shoot grows into the
-  ground; the crown frame the shoots' phototropism reads follows the living crown.
-- **The pine preset** is one shoot rule from the stem out [KK1991 Tables 3-4, Fig. 2], 30 seasons.
-
-**Measured against the gate (seed 1337):**
-
-| | master | S1 |
-| :--- | ---: | ---: |
-| height | 10.7 m | 12.2 m |
-| DBH | 73 cm | 25 cm |
-| H/D | 15 | 48 |
-| crown width | 5.0 m | 10.9 m |
-| leaf | 16 m² | 279 m² |
-| side density / transparency | 0.34 / 0.64 | 0.57 / 0.33 |
-| nodes | 5,374 | 81,890 |
-
-- **Height and girth.** H/D 48 falls in the 40-55 the open-grown evidence suggests (stand-grown pine runs 52-89;
-  Kellomäki 1984, Hu et al. 2020). The leader's onset in Eq. 6 is refitted to open-grown heights: KK1991's 11.16
-  extrapolates below their 1.1 m smallest tree and takes 15 years to the first metre; 4.34 fits eleven open-grown
-  trees of known age (Kuuluvainen et al. 1988; Sievänen et al. 1997), RMS 1.3 m, 11.1 m at 30 years against 11.4 m.
-- **Leaf over the forest allometry.** 279 m² against 36-63 m² for a forest pine of DBH 25 cm; but the target is
-  forest-grown and this tree carries its crown to the ground.
-- **Against an open-grown checkpoint** (Kuuluvainen et al. 1988, Table 3: age 8, 2.73 m tall, crown 1.70 m wide,
-  1.38 kg of needles, 110.6 m of shoots, 9.4 branches a whorl), the seedling pine at about 2 m: crown 1.3-1.8 m wide;
-  18-23 m of shoots and 0.27-0.34 kg of needles; 7-16 living boughs.
-- **Other presets** moved with the shared changes: oak 89 → 80 m², maple 51 → 56, willow 233 → 249, shrub 63 → 71.
-- **Specs:** 12 fail, all reading pine's old structure (inter-whorl branches, graph tiers and stubs, the graph trunk's
-  L/D bound of 26, its righting reflex). The stem leans 0.16 where the graph's trunk held 0.08.
-
-**Two measured defects remain, both forks:**
-
-- **F6, the stem's whorl.** The stem bursts KK1991's 3.99 + 0.022 L daughters, and the shedding then keeps each at
-  Rb / yield ≈ 0.45, with Rb = 1.867 measured on a branch (Niinemets & Lukjanova 2003). So about one bough survives
-  a year, against 9.4 living branches a whorl on open-grown trees (Kuuluvainen et al. 1988) and 5-6 in young stands
-  (Kellomäki 1984). KK1991's counts are living shoots already.
-- **F7, the boughs never slow.** A bough's first shoot is 0.570 of the stem's (27 cm under a 47.5 cm leader), and each
-  terminal 0.995 of the last, so a bough grows ~27 cm a year for its life: 5-6 m boughs at 25 years and a crown 10.9 m
-  wide. KK1991 say so themselves and cap a branch's length by a stand-grown fit (Eq. 9, Bmax 142 ± 44 cm, Kellomäki
-  et al. 1988). Light does not bind: bough tips see 0.8-0.96 of open sky in the young tree, median 0.81 at 30 years,
-  so shoot length by light (Niinemets & Lukjanova 2003, Fig. 3B) would barely shorten them. Drawing KK1991's
-  terminal ratios with their measured spread (cv 44-58%) was tried and reverted: independent ratios make a
-  heavy-tailed random walk (crowns 2.4-4.6 m wide across three seeds at the same age), which KK1991's model is not.
-
-## Decisions on F6 and F7 (Alex, 2026-10-26: "parametric, principled, broadly general, one code path; you choose")
-
-- **F6: full light keeps every shoot the bud demography gives.** Rb at saturation is the gross yield of the unit a
-  shoot grows on (`shoot_expected_yield` at that unit's length), not a per-species constant; it falls to 1 at the
-  compensation light and below it as before, so a new shoot survives at `Rb(Q) / yield`, 1 in full light. This is
-  what maple's net counts and the shrub's gross yield already did by hand, made the rule; `ShootGrowthConfig.vigour`
-  goes. The per-species Rb measurements become cross-checks.
-- **F7: Borchert-Honda apical control** (Palubicki et al. 2009, *ACM TOG* 28(3): 58, after Borchert & Honda 1984).
-  Each season the light each axis's tip receives is summed down every subtree to the carrier; it flows back up, and
-  at each node the continuing axis takes a share weighted `λ` and the laterals `1 − λ`. A shoot's unit is its
-  demographic mean length times its vigour per unit of its own light. At `λ = 0.5` that ratio is 1 everywhere, so a
-  species with no fitted `λ` grows as before on the same code path. Pine's `λ` is fitted to the open-grown crown of
-  Kuuluvainen et al. (1988, Table 3): 1.70 m wide at 2.73 m tall. The stem keeps its height-driven leader.
-
-## After F6 and F7 (seed 1337, uncommitted)
-
-Built as decided, plus two fixes the stem's lean exposed:
-- **Phototropism follows the light field.** A shoot turns towards where the field grows brighter (its gradient), not
-  away from the crown frame's centre: that pushed a lopsided crown's leader further off, a feedback that leaned the
-  stem 0.15. `shoot_outward3` is gone; the crown frame still follows the grown crown for the foliage and its shading.
-- **Zigzag kinks a unit, not the course.** An axis's heading carries its tropisms; each unit is kinked off it by the
-  generator's zigzag. Accumulated into the heading, the zigzag was a random walk.
-
-| | master | S1 now | target |
-| :--- | ---: | ---: | :--- |
-| height | 10.7 m | 10.9 m | 11.4 m at 30 years, open-grown |
-| DBH, H/D | 73 cm, 15 | 15 cm, 70 | 40-55 open-grown (estimate); 52-89 stands |
-| crown width | 5.0 m | 7.3 m | unknown for an open-grown 11 m pine |
-| leaf | 16 m² | 70 m² | 15-25 m² for a forest pine of DBH 15 cm |
-| side density / transparency | 0.34 / 0.64 | 0.44 / 0.54 | 0.45-0.51 / 0.15 |
-| stem lean | | 0.004-0.020 over 7 seeds | spec: under 0.08 |
-
-At the open-grown checkpoint (Kuuluvainen et al. 1988, Table 3) the 12-year pine, 2.6-3.5 m tall, has a crown
-0.59-0.64 of its height (0.62) and 56-107 m of shoots (110.6 m at 2.73 m).
-
-**Other presets** under F6 (full light keeps every shoot): oak 80 → 110 m² and density 0.47 (in band), maple 56 → 84 m²
-and 0.46 (in band), birch 74 → 61, willow 249 → 236, spruce 81 → 84, shrub 71 → 42 (its partial-light Rb now ramps to
-each unit's own yield, not to the yield at its mean length).
-
-**Specs: 15 fail.** Pine's old structure: inter-whorl branches, graph tiers and stubs, the graph trunk's L/D bound of
-26 and its crookedness, the conical spire, a plagiotropic trunk's knocked-out buds, branch crossings (shoots do not yet
-keep out of each other's wood, design 3), bark relief on boughs, preset traits. Oak: the wind spec compares a leafy and
-a bare oak, which now grow different wood (no leaves, so full light everywhere, so every shoot kept), and one oak spec
-timed out at 60 s under load.
-
-## S1 finished: shoots keep out of older wood, specs restated (2026-10-27, uncommitted)
-
-**Shoots keep out of all older wood** (design 3), in `ShootWoodHash` beside `ShootFrameworkHash`:
-- **The hash.** Every grown annual unit is added once under the cells its line crosses (0.1 m, about a twig's unit;
-  measured against 0.25 and 0.05 m). A query reads each unit's place and radius as they are, padded by the thickest
-  wood, so thickening needs no re-adding. Exact pre-filters: a unit nowhere as thick as the probe needs, a padded box
-  test, and each cell's thickest living unit, refreshed once a season.
-- **Blocked buds.** A new unit does not grow into the ground, framework wood, or older shoot wood it does not join. A
-  blocked bud turns by the golden angle round its node, as the plagiotropic knockout already did; a blocked terminal
-  waits a season.
-- **Junctions.** One wood with: its mother either side of where it grew and over its crotch (nearer her axis than her
-  radius); its grandmother where it grew at its mother's base; a carrier's extension and the carrier's laterals by its
-  tip; siblings' first units within the collar they share (out of the mother's wood, at least half way, as the
-  interpenetration spec always held siblings).
-- **Engulfed and buried.** A shoot whose line thicker wood (or as thick and older), compared where they meet, has
-  grown into dies. So does a lateral whose tip the wood its mother grew since has closed over: one that grew out of
-  wood already there, as on a carrier the graph laid at its full girth, is not buried. A carrier its parent has grown
-  over dies with its twigs; a graph branch the thickening buries is dead, an occluded knot, not a stub.
-- **Leaves pay.** A lateral of a generator that bears no leaves (no foliage rule) does not grow. Under F6 a crown that
-  casts no shade kept every bud and grew by its gross yield every year (an oak with `foliage_rules: []` took 92 s). Every
-  preset's shoot generators bear leaves, so no preset changes.
-- **Plagiotropism and straightness** turn a shoot's course as they turn the graph's spines (design 5); a stem is a
-  trunk and takes neither, nor knocks out its buds.
-
-**Measured (seed 1337):**
-
-| preset | leaf | side density | transparency | skeleton |
-| :--- | ---: | ---: | ---: | ---: |
-| pine | 62 m² | 0.43 | 0.57 | 1.4 s |
-| oak | 102 m² | 0.49 (in band) | 0.39 | 0.5 s |
-| maple | 81 m² | 0.45 (in band) | 0.37 | |
-| spruce | 52 m² | 0.30 | 0.31 | 2.7 s |
-| birch | 58 m² | 0.54 | 0.35 | |
-
-Pine: 10.8 m, DBH 15 cm, H/D 73, crown 7.3 m wide; 78k nodes, 641k triangles. The open-grown checkpoint still holds
-(crown 0.54-0.66 of height at 12 years, 0.62 measured). Stem lean 0.001-0.011 over seven seeds.
-
-**Specs.** Restated from their principle:
-- pine's traits: the graph lays only roots, one shoot rule grows the stem and all on it;
-- the spire is the leader's newest unit and what grows on it (the trunk's unit record);
-- the trunk's apex is no thicker than a current shoot of its newest unit's length;
-- per-unit slenderness for any branch the shoots grew on past its generator's length; sweep only for trunks the
-  graph grew;
-- a split fork is the graph's: same depth and generator, not a shoot rule's;
-- tiers come from a whorl: the graph's whorled rules, or a shoot's buds all under its terminal bud;
-- spruce's twigs fan in from whorl and inter-whorl boughs; the pine's stem bears its boughs and its boughs the twigs;
-- stubs are dead graph wood that sticks out of the bark, grown without the twig layer; pine grows none yet (S3);
-- foliage collection and the wind rig read the same oak, grown in the shade of its own leaves;
-- interpenetration: every child has a crotch; shoots are held to "no line inside other wood", spurs aside; a twig on a
-  carrier the graph laid at full girth is not buried;
-- bark relief compares every consecutive pair of trunk rings of one vertex count; the youngest bark is on any shoot;
-- senescence follows the crown's mean dryness, the most dried card bounding it;
-- the tiers spec grows twelve conifers with their foliage and has 180 s.
-New: `tree_skeleton_grow_seedling.spec.js` (leader by height, one stem from the ground, height at age, no shoot in the
-ground, carriers growing on, apical control), `ShootWoodHash.spec.js`, survival (`shoot_survival`), dead wood bears no
-shoots, a leafless generator grows no laterals.
-
-**Mutation testing**: 23 of 28 mutants killed. Survivors, each measured:
-- **Blocked buds and extensions, the sibling collar for blocking** (three): at season's end engulfment kills whatever
-  grew through older wood, so the final trees cannot tell. The blocking is kept for what it changes: without it the
-  pine's crown is 8.7 m wide against 7.3, and spruce carries 33 m² against 39.
-- **A carrier buried during the simulation**: no preset has a buried carrier that grows twigs (spruce's one starts
-  inside its mother's wood, so its buds are blocked). "Dead wood bears no shoots" would catch it.
-- **The light field following the crown**: without it the pine's upper crown sees open sky and carries 71 m² against
-  62. No spec reads the shading.
-
-**Open, measured:**
-- **Pine's crown is see-through:** transparency 0.57 against FIA's 0.15. Its leaf is 4.5x a forest pine's of its DBH,
-  so S2's girth from leaf will move DBH, not the crown.
-- **No open-grown target for crown width** at 11 m.
-- **Cost:** spruce's skeleton 2.7 s, most of it the engulfment pass; the gate's spruce 4.8 s against master's 3.8.
-- **Mesh size:** 5k → 78k nodes for the pine.

package/src/generation/foliage/SHOOT_SYSTEMS_ALL_SPECIES_BRIEF_2026_10_26.md

@@ -1,248 +0,0 @@
-# Shoot Systems for Every Woody Species
-
-Follows `ANNUAL_SHOOTS_BRIEF_2026_10_25.md`, which grew the oak's twigs year by year and put its leaves on them.
-
-## Problem
-
-Only the oak grows a twig layer. The other woody presets still hang their leaves on cards of 0.7-1.3 m, drawn by the
-density rule along their framework branches. The oak's model cannot simply be copied: it hard-codes four oak facts.
-
-| What the oak model assumes | Where | Species where it is false |
-| :--- | :--- | :--- |
-| Leaves live one season, on the current unit only | `foliage_collect_attachments`, joint mechanics | pine (needles kept 3-4 years), spruce (7-9) |
-| Leaves crowd at the unit's tip: one card a unit | `MEDIAN_CURRENT_SHOOT_LENGTH`, the `rosette` arrangement | willow and birch long shoots (leaves along the shoot), conifers (needles along it) |
-| Every bud that grows out makes an axis that extends every year | `shoot_demography_grow` | maple and birch: most buds become short shoots, which grow millimetres a year and leaf every year |
-| Oak's bud zones, length distributions and wood diameter | `SUBAPICAL_U_*`, `MEDIAN_U_*`, `NEGATIVE_BINOMIAL_P`, `shoot_radius` | every other species |
-
-**Baseline**, seed 1337, master `ee5c666c3`, crown fullness from a raster fitted to the leaves (the side opacity is over
-pixels within 10 cm of a leaf):
-
-| preset | cards | median card | leaf area | side opacity | LAI over top silhouette |
-| :--- | ---: | ---: | ---: | ---: | ---: |
-| oak | 2,261 | 0.17 m | 93 m^2 | 0.49 | 3.2 |
-| pine | 693 | 0.76 m | 174 m^2 | 0.69 | 5.5 |
-| birch | 399 | 0.72 m | 45 m^2 | 0.44 | 3.2 |
-| willow | 1,455 | 1.27 m | 241 m^2 | 0.67 | 4.5 |
-| maple | 478 | 0.88 m | 150 m^2 | 0.66 | 3.9 |
-| spruce | 1,191 | 0.69 m | 161 m^2 | 0.57 | 4.7 |
-| shrub | 114 | 0.56 m | 10 m^2 | 0.48 | 1.5 |
-
-## Scope
-
-- **Woody presets get shoot systems:** oak, pine, birch, willow, maple, spruce, shrub.
-- **Palm and fern do not.** A palm grows from one apical meristem and never branches. A fern's fronds rise from its
-  rhizome. Neither has a twig system, and their frond cards already draw single leaves at real size (palm 1.85 m,
-  fern 0.95 m).
-- **Species each preset stands for.** These are needed to pick sources.
-  - **oak:** *Quercus robur / petraea* (unchanged).
-  - **pine:** *Pinus sylvestris*, as its comments already say.
-  - **spruce:** *Picea abies*.
-  - **birch:** *Betula pendula* (white bark, pendulous twigs).
-  - **maple:** *Acer rubrum*. Its anthocyanin potential of 0.9 is a red-autumn maple, and red maple has the best data.
-  - **willow:** a weeping willow (*Salix babylonica*, *S. x sepulcralis*), with pendulous-willow and *S. alba* data.
-  - **shrub:** *Corylus avellana* (hazel), which matches its multi-stemmed habit and ovate leaves. The preset names no
-    genus today; this is my pick.
-
-## Sources
-
-Read in the paper itself unless marked. "2nd" is second-hand (abstract or citing paper), and "summary" was read
-through a web summarizer and must be checked before it goes into code.
-
-**Red maple.** [W1966] Wilson, B.F. (1966). Development of the shoot system of *Acer rubrum* L. Harvard Forest Paper
-14. 38 felled trees up to about 115 years old. [C1971] Critchfield, W.B. (1971). Shoot growth and heterophylly in
-*Acer*. J. Arnold Arboretum 52(2): 240-266. [G1980] Gregory, R.A. (1980). Can. J. For. Res. 10: 316-326 (sugar maple).
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Long vs short shoot | long elongates > 2 cm a year and bears laterals; short < 2 cm, none; either can become the other | W1966 p. 2 |
-| Short shoots, share of all shoots | 85-95% | W1966 abstract, p. 10 |
-| New laterals a long shoot yields a year | order 2 on the stem: 1.8 long + 4 short; 3rd/2nd: 1.5 + 4; 4th/3rd: 0.1 + 4; 5th/4th: 0.03 + 4 | W1966 p. 10, Table 2 |
-| Bud fates along a 1-year shoot | top pairs long, middle pairs short, lowest pair may abort | W1966 p. 3, Fig. 1 |
-| Annual length increment by order 2-6 | 8.8, 4.5, 3.6, 3.4, 2.7 cm | W1966 p. 6 |
-| Leaf nodes on last season's shoot | long 7.8 (4-11), short 2.0 (1-3) | C1971 Table 1 |
-| Leaves per shoot by order | long 16, 14, 12, 8, 6 (orders 1-5); short 6 (orders 2-5), 4, 2 | W1966 Table 4 |
-| Area per leaf | long shoot 14-64 cm^2; short shoot 10-44 cm^2 | W1966 Table 4 |
-| Leaf area from length | log A = 0.0898 + 1.81 log L | W1966 p. 6 |
-| Petiole | 0.6-1.14 of the blade (early leaves), 0.3-0.8 (late) | C1971 p. 256 |
-| Survival | 1-6 (mean 2) live 2nd-order long shoots per annual group; shaded branches die | W1966 Fig. 7, p. 19 |
-
-**Silver birch.**
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Short shoot | one bud; two or three leaves a year; grows a couple of millimetres a year; carries most of the foliage; can become a long shoot | Jones & Harper 1987, Proc. R. Soc. B 232: 19-33 (2nd); Kull et al. 2003, Ann. Bot. 91: 559-569, pp. 560-561; Lintunen 2013, Diss. For. 165, p. 27 |
-| Short shoots | never sylleptic; in the upper crown at the base of last year's shoot | Kull et al. 2003 p. 567 |
-| Long shoot | many buds on elongated internodes; long-shoot lengths 0-120 cm, order means 0-30 cm (figure only) | Jones & Harper 1987 (2nd); Lintunen 2013 Fig. 7 |
-| Short shoots per branch | 46-54 | Lintunen 2013 Table 3 |
-| Leaf blade | 3-7 x 2.5-5 cm | Flora of North America vol. 3 |
-
-**Willow.**
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Bud fates, pendulous willow ('Prairie Cascade', young trees) | 40% sylleptic, 29% proleptic shoots | Remphrey & Pearn 2006, Can. J. Bot. 84: 1531-1541 (2nd, abstract) |
-| Shedding, same | 7% of shoots in year 1, more than half by year 3, survivors on the parent's upper half | same |
-| *S. alba* annual shoots | 5-25 cm, at 30-60 degrees; no sylleptic shoots; no short shoots | Héja 2007, Tilia 13: 77-94, p. 82 |
-| Cladoptosis | shoots shed in autumn through an abscission zone, mostly 1-2 years old | Héja 2007 pp. 79-80 |
-| Leaf blade | *S. babylonica* 9-16 x 0.5-2 cm; *S. x sepulcralis* 7-14 x 0.9-1.8 cm | Flora of North America vol. 7; JANAS 29(1) |
-
-**Scots pine.**
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Net shoots per last year's shoot on a branch (Rb) | 1.35-1.42 in low light, rising with light and with shoot length; constant over a branch's life | Niinemets & Lukjanova 2003, Ann. For. Sci. 60: 195-208, pp. 198-200 |
-| Needle sets kept | 3.7 (S. Finland), 2.8 (Estonia); median shed at 4 years, 15% reach 5 | Pensa & Jalkanen 1999, Silva Fennica 33: 171-177, pp. 173-175 |
-| Needle length | 52 mm (fertile site), 25 mm (bog); unchanged with age | Niinemets & Lukjanova 2003 Table I |
-| Fascicles per cm (leaders) | 7.8 (6.9-8.5 stand means) | Salminen & Jalkanen 2006, Silva Fennica 40: 183-194, Table 3 |
-| Branching | stops at relative light 0.20-0.25; negligible below 0.6 of tree height | Ilonen et al. 1979, Silva Fennica 13, pp. 319-321 |
-
-**Norway spruce.**
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Bud fates on 1-year shoots, healthy trees | about 64% flush, 30% dormant but viable, 6% abort | Polák et al. 2006, For. Ecol. Manage. 225: 337-348, p. 344 |
-| Needle retention | 7-9 years; 50% of a cohort shed by 5.5 years, all by 12 | Polák et al. 2006 p. 342; Muukkonen & Lehtonen 2004 (2nd) |
-| New shoot, needles | mean 4.8 cm (2.2-11.3); 18-31 needles per cm | Bellan et al. 2019, Austrian J. For. Sci. 136: 1-26 |
-| Whorl zone | whorl branches in the top 20% of a unit; internodal branches short-lived | Colin & Houllier 1992, Ann. Sci. For. 49: 511-538 |
-| Shoot to mother angle | 60% between 40 and 70 degrees | Fabrika et al. 2019, BioResources 14: 908-921, Table 7 |
-
-**Hazel.** Grisafi et al. 2024, in silico Plants 6(1) diae004 (open access; read through a summarizer, to verify):
-1.13 buds a node; vegetative bud burst 0.97 distal to 0.62 proximal; shoot from a vegetative bud mean 4.1 cm; 8 nodes
-on 10-25 cm shoots; the apical bud dies (sympodial). An orchard cultivar. Leaf area 41 cm^2 in sun (Catoni et al.
-2015, Photosynthetica 53: 35-46, Table 2).
-
-## Sources supplied 2026-10-26
-
-Alex supplied the paywalled papers. Each was read in full except where a figure is "read approximately".
-
-**[M1982]** Maillette, L. (1982). Structural dynamics of silver birch. I. The fates of buds; II. A matrix model of the
-bud population. *J. Appl. Ecol.* 19: 203-218, 219-238. Three mature open-grown trees, 4-10 m, North Wales; about
-13,000 buds.
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Buds per long shoot | mode 4, on its late leaves only | I p. 213, Fig. 9 |
-| Leaves per long shoot | mode 6 | I p. 213 |
-| Long-shoot length | modal class 51-100 mm | I p. 210, Fig. 6a |
-| Long-shoot apex | always aborts; growth is sympodial | I p. 206 |
-| Short shoot | < 3 mm a year; two or three leaves; one bud; "a large proportion died"; few become long | I pp. 205-213 |
-| Leaves on short vs long shoots | B1 12,000 / 10,000; B2 5,300 / 3,100; B3 3,000 / 1,300 (figure) | I Fig. 2 |
-| Bud population growth a year (lambda) | whole crown 1.38; top 1.52; bottom 0.999 | II Table 1 |
-
-**[JH1987]** Jones, M. & Harper, J.L. (1987). The influence of neighbours on the growth of trees. II. The fate of buds
-on long and short shoots in *Betula pendula*. *Proc. R. Soc. Lond. B* 232: 19-33. Four-year-old trees in open
-grassland; values for the low-interference zone.
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Long-shoot buds becoming long shoots | about 50% on the youngest branches; 16-26% on older ones | pp. 21-22, Fig. 2 |
-| Buds surviving a year | 62% (year 2), 57% (year 3) | p. 26 |
-| Leaves per long shoot | commonly 4-8; internodes 15-25 mm | pp. 19-20 |
-
-**[KK1991]** Kellomäki, S. & Kurttio, O. (1991). A model for the structural development of a Scots pine crown based on
-modular growth. *For. Ecol. Manage.* 43: 103-123. 25 trees, 7-19 years, eastern Finland. Order 0 is the stem.
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Daughter shoots (terminal included) of a shoot L cm long | k + c L; order 0: 3.99 + 0.022 L; 1: 0.992 + 0.161 L; 2: 0.544 + 0.149 L; 3: 0.861 + 0.041 L | Eq. 1, Table 3 |
-| Lateral length / parent length, by parent order 0-3 | 0.570, 0.458, 0.355, 0.475 | Table 4 |
-| Terminal length / parent length, orders 0-4 | 1.196, 0.995, 0.913, 0.938, 0.999 | Table 4 |
-| Branching angle, orders 1-4 | 83, 61, 59, 65 degrees | Fig. 2 |
-| Needles surviving, by age 1-4 | 1, 0.90, 0.69, 0.22; a shoot without needles dies | p. 113 |
-
-**[KS1995]** Kellomäki, S. & Strandman, H. (1995). *Ecol. Model.* 80: 237-250. Needle length 0.4 L for shoots under
-10 cm, 4 cm above (Eq. 17).
-
-**[L2011]** Lintunen, A., Sievänen, R., Kaitaniemi, P. & Perttunen, J. (2011). Models of 3D crown structure for Scots
-pine and silver birch grown in mixed forest. *Can. J. For. Res.* 41: 1779-1794. Birch long shoot in branches: 14.6 cm,
-6 leaves of 11.8 cm^2; short shoots modelled with 2 leaves (Table A2, B20).
-
-**[NL2003]** Niinemets, Ü. & Lukjanova, A. (2003). *New Phytol.* 158: 75-89.
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Rb, net shoots per last year's shoot | *P. abies* 0.65-2.19 (example branch 1.516); *P. sylvestris* 0.98-4.17 | Table 1, Fig. 2 |
-| Rb against light | rises steeply with light; below 1 in deep shade | Fig. 5b |
-| Needle survival, *P. abies*, ages 2-9 | about 0.93, 0.93, 0.80, 0.76, 0.70, 0.57, 0.55, 0.19 (figure) | Fig. 4 |
-| Current shoot, *P. abies* | 0.6-4.6 cm, longer in light (figure) | Fig. 6 |
-
-**[H2007]** Hein, S. et al. (2007). *For. Ecol. Manage.* 242: 155-164. Norway spruce: 6.03 branches a stem whorl
-(4,851 over 804 whorls). Stem whorls only.
-
-**[RP2006]** Remphrey, W.R. & Pearn, M.A. (2006). Crown architecture development in *Salix* 'Prairie Cascade', a
-pendulous willow. *Can. J. Bot.* 84: 1531-1541. Young trees from cuttings.
-
-| Quantity | Value | Where |
-| :--- | :--- | :--- |
-| Terminal bud | aborts each year: sympodial | p. 1532 |
-| First-year shoot | 1,104 mm, 42 nodes | p. 1533 |
-| Bud fates | sylleptic 40.1%, proleptic 29.3%, aborted 24.6%, dormant 6.0% | Table 1 |
-| Laterals still present | 93% in year 2, 58% in year 3, 46% in year 4; the lowest quarter of the parent sheds almost all | p. 1535, Table 2 |
-| Current shoots in summer | hang at -80 to -88 degrees | Fig. 7 |
-
-## Gaps that remain
-
-| Missing | Species | Treatment |
-| :--- | :--- | :--- |
-| Lateral buds per shoot, lengths by order | spruce | pine's [KK1991] counts and ratios, stated as borrowed |
-| Short-shoot annual survival | birch, maple | birch: [JH1987]'s bud survival (0.6); maple: fitted to [W1966]'s 85-95% short-shoot share |
-| Shoot diameter | all but oak | [BB2000] Table 7 for every species |
-| Needle length | spruce | not found; chosen |
-| Hazel numbers | shrub | [Grisafi 2024] read through a summarizer only; to verify |
-
-## Design
-
-The oak's model, generalised. Every number becomes a `ShootSystemRule` field; the oak's defaults stay, and the oak's
-output is bit-identical after the refactor (checked against a fingerprint of three seeds).
-
-1. **Per-order arrays.** Lengths, outgrowth and insertion angles differ by branching order in every source, so these
-   fields hold one value per order, the last repeating.
-2. **Unit length** is `intercept[order] + slope[order] x parent unit length`, drawn as the oak's (1 cm plus a negative
-   binomial or Poisson count of centimetres, capped per order). The oak has slope 0 and intercepts from [BB2000];
-   pine has intercept 0 and [KK1991]'s ratios. Maple uses [W1966]'s means by order.
-3. **Bud zones** (`ShootBudZone`): where on the unit (u range), how many buds (`buds + buds_per_metre x length`),
-   and per order the share growing a long shoot next year, a sylleptic shoot this year, or a short shoot. The
-   oak's two zones are its subapical and median buds.
-4. **Sylleptic shoots** (willow) grow out in the same season as their mother unit, so a fast shoot branches at once.
-5. **Short shoots** (birch, maple) are a bud fate: a single-segment branch that grows `short_shoot_growth` a year, has
-   no laterals, leafs every year, and survives a year at `short_shoot_survival`. A shed mother takes them with it.
-6. **Vigour is Rb**, the net shoots a shoot leaves a year: sourced for pine and spruce [NL2003], birch (lambda,
-   [M1982]) and maple ([W1966]'s net yields); chosen for oak and willow.
-7. **Leaf cohorts.** `leaf_survival[age]` is the share of a unit's leaves alive at each age: `[1]` for the deciduous
-   species, [KK1991] for pine, [NL2003] for spruce. The skeleton records where each recent unit of a branch starts,
-   replacing `branch_current_growth_t`.
-8. **Cards tile the leafy units.** Each card covers the stretch of shoot its tile draws (`card_length * stem_length`),
-   scaled within 0.6-1.6 so a whole number fits, thinned by the cohort's survival. The oak keeps about one card per
-   unit. Short shoots carry one card at their tip.
-9. **Cards at real size.** The card length follows from the species' leaf length and how long its arrangement draws a
-   leaf in a tile. The leaves a card draws follow from the leaves per metre of shoot.
-10. **Two tile kinds** where a species has short shoots: the atlas draws its sprays (long-shoot stretches) and its
-    rosettes (a short shoot's 2-4 leaves) as separate variant sets, so neither card carries the wrong leaf count.
-
-## Crown fullness (the next question)
-
-The best measured target found: the US Forest Inventory's crown ratings, 15,011 leaf-on trees seen from the side
-(Randolph 2006, USDA GTR SRS-94, Tables 1-4).
-- **Crown density.** Branches and foliage block a mean 45% of the crown's outline (oaks, maples, birches 46-51%).
-- **Foliage transparency.** Within the foliated parts, only about 15% of skylight comes through, so they are 80-85%
-  opaque.
-
-So a healthy crown is dense clumps that fill about half its outline. Our probe measures opacity within 10 cm of a leaf,
-which is nearer the clumps: the oak reads 0.49 there against about 0.85. This is measured after the propagation, as
-asked.
-
-## Plan
-
-1. Generalise `ShootSystemRule` and `shoot_demography_grow`: zones, per-order arrays, syllepsis, short shoots. The
-   oak's fingerprint is unchanged.
-2. The writer: short shoots, opposite phyllotaxis, per-order angles; the unit record.
-3. Foliage and mechanics: leaf cohorts, tiled cards, short-shoot cards, tile kinds.
-4. Presets: pine, spruce, birch, maple, willow, shrub, each with carriers, a twig generator, a sourced rule and
-   real-size cards.
-5. Specs per species against their sources, mutation-tested.
-6. Measure every preset and look at each in the playground.
-
-## Landed (2026-10-26, uncommitted)
-
-Every woody preset grows its twigs from `shoot_rules`, each with its own `ShootGrowthConfig`, and the crown fills by
-light. What landed, the specs restated and the measured crowns are in `CROWN_FILLING_BRIEF_2026_10_26.md`.