[Manure] Adds option for partial emptying of manure storages

[matthew7838]

Adds an optional emptying_fraction input to manure storage configs so storages can be partially emptied, and fixes partial-emptying routing so the emptied manure (not the retained manure) is what leaves the storage.

Context

Issue(s) closed by this pull request: closes #2963

Related: #3228 plans to treat the Manure.Storage.*emptied_manure_* outputs as sold manure in the economics module. This PR keeps those outputs consistent for that use: at every emptying event, the emptied_* variables report exactly the manure removed from the storage, whether the emptying is full or partial.

What

• New optional storage config key emptying_fraction (0.0-1.0): the fraction of stored manure removed at each scheduled emptying event. Supported by all storage types except DailySpread. Omitted, behavior is unchanged (full emptying; anaerobic lagoons keep their default sludge retention).
• Fixes a partial-emptying bug from [Manure] Updates Contributing Factors to Anaerobic Lagoon Methane Calculations #2638: Storage.process_manure() returned the retained stream for downstream routing instead of the emptied stream, so the emptied manure vanished from the processor chain and the retained manure was duplicated (kept in storage and passed downstream). Currently this affected anaerobic lagoons, which empty fractionally by default.

Why

Users have asked to simulate manure storages that are not fully emptied (X% emptied per emptying interval, #2963). The _emptying_fraction hook added in #2638 already splits the stored manure but was not user-configurable. The routing fix is also a prerequisite for #3228: "emptied = sold" only holds if the emptied stream is what actually leaves the storage.

How

• Storage.__init__ accepts emptying_fraction and validates it to [0.0, 1.0] at initialization; the _emptying_fraction property returns the configured value when provided, otherwise the class default (1.0; anaerobic lagoons: 1 - ANAEROBIC_LAGOON_MANURE_RETENTION). All storage subclasses except DailySpread pass the parameter through.
• On partial-emptying days, Storage.process_manure() now returns the emptied stream for routing to connected processors; the retained stream stays in stored_manure.
• Added emptying_fraction to the storage properties in RUFAS/input/metadata/properties/default.json, range-checked during input validation.
• Regenerated the open_lot e2e manure expected results: with the routing fix, the lagoon's emptying-day accumulated_* and storage_methane are computed on the emptied stream (day 364; values increase ~9x since the lagoon empties 90%). emptied_manure_* values are unchanged.

Test plan

• New unit tests: partial (0.25/0.9) and zero emptying fractions in Storage.process_manure assert the emptied stream is reported and returned while the retained stream stays stored; init-time validation of out-of-range fractions; lagoon default retention vs. configured override.
• Input pipeline verified with a real InputManager run on a modified open_lot config: emptying_fraction: 0.4 loads and reaches the constructed storage; 1.5 is rejected at input validation.
• 60-day open_lot simulation with lagoon emptying_fraction: 0.4 and storage_time_period: 10: on every emptying day the emptied mass and nitrogen are exactly 0.4 of the stored amount, the retained 0.6 stays in storage, and day-over-day storage balance holds.
• Full manure unit test suites pass (389 tests); input manager/data validator suites pass (718 tests).
• Open_lot end-to-end comparison run locally against the regenerated expected results: Manure, Animal, and Feed pass. CropAndSoil shows a day-0 manure_type dictionary-item-added failure that reproduces identically on plain dev (verified in a clean dev worktree), so it is pre-existing and unrelated to this change; its recorded expected results are untouched by this PR.

Input Changes

• New optional emptying_fraction key for storage configs in the manure_management input (all storage types except DailySpread). Existing inputs are unaffected.

Output Changes

• No new output variables. With the routing fix, on partial-emptying days Manure.Storage.*.accumulated_* and Manure.Storage.*.storage_methane reflect the emptied stream instead of the retained stream. Only storages with fractional emptying are affected - currently anaerobic lagoons, once per storage_time_period.

Filter

{
  "name": "lagoon_emptying",
  "filters": ["Manure.Storage.AnaerobicLagoon.*"]
}

[github-actions]

Current Coverage: 99%

Mypy errors on manure-partial-empty branch: 1136
Mypy errors on dev branch: 1133
3 more errors on manure-partial-empty branch

[github-actions]

🚨 Please update the changelog. This PR cannot be merged until changelog_WIP.md is updated.

[github-actions]

Current Coverage: 99%

Mypy errors on manure-partial-empty branch: 1167
Mypy errors on dev branch: 1164
3 more errors on manure-partial-empty branch

[github-actions]

Current Coverage: 99%

Mypy errors on manure-partial-empty branch: 1164
Mypy errors on dev branch: 1164
No difference in error counts

[github-actions]

Current Coverage: 99%

Mypy errors on manure-partial-empty branch: 1164
Mypy errors on dev branch: 1164
No difference in error counts

[github-actions]

Current Coverage: 99%

Mypy errors on manure-partial-empty branch: 1164
Mypy errors on dev branch: 1164
No difference in error counts

[github-actions]

Current Coverage: 99%

Mypy errors on manure-partial-empty branch: 1164
Mypy errors on dev branch: 1164
No difference in error counts