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sci.1.84.1_api.40.0.0

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Adjustment to trim logic

This partially addresses #1393

sci.1.84.0_api.40.0.0

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updates to the default parameter file

This update includes a phenology parameter refactor per #1355, an update
to the default exclusion parameter per #1358, updates to the logging
parameters to default to clearcut via #1359, and a minor long name
correction per #1394.

sci.1.83.1_api.39.0.0

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refactor and stardardize per-ageclass history

sci.1.83.0_api.39.0.0

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two-stream sun-shade fraction update

This simplifies the leaf sunlit fraction calculation to assume that it
is comparible to that of other media.

sci.1.82.8_api.39.0.0

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Refactor of vegetation bin indexing.

sci.1.82.7_api.39.0.0

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fix to trivial radiation transmission bug

sci.1.82.6_api.39.0.0

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This set of changes is a bugfix. The units on excess respiration mass…

… balance checking were incorrect, and the history diagnostics associated it also had an incorrect unit.

sci.1.82.5_api.39.0.0

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Add site x pft expansions of seed bank and related history output

sci.1.82.4_api.39.0.0

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Correct missing understory fire-induced carbon flux to history output

sci.1.82.3_api.39.0.0

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Fixes to two-stream to allow restart tests to pass, changed zenith an…

…gle boundary conditions to the site level and removed the zenith flag.
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