_user_input_keys drifts from stored values after delete_arrays and clone #559

Simulation._user_input_keys, the (variable, branch, period) record of values set with set_input, drifts from the stored arrays in two ways (3.32.9):

1. delete_arrays keeps the entries for the arrays it deletes. A formula result calculated later for the same period is then treated as a user input. _invalidate_all_caches (run by apply_reform) replays it, so the stale formula output survives a reform, and to_input_dataframe would export it.
2. clone() shares the set with the original (the shallow __dict__ copy) while the holders' stored arrays are copied. An input set later on the clone is then recorded for the original as well, and on a parent after get_branch it is recorded for branches created earlier, whose storage never received it.

Reproduction with the country template:

from policyengine_core.country_template import CountryTaxBenefitSystem
from policyengine_core.simulations import SimulationBuilder

tbs = CountryTaxBenefitSystem()
def sim():
    return SimulationBuilder().build_from_entities(
        tbs, {"persons": {"a": {"salary": {"2025-01": 1000}}}, "households": {"h": {"parents": ["a"]}}})

s = sim()
s.set_input("income_tax", "2025-01", [5.0])
s.delete_arrays("income_tax")
s.calculate("income_tax", "2025-01")          # formula output, 150
s._invalidate_all_caches()
print(s.get_holder("income_tax").get_array("2025-01"))   # [150.] replayed as if it were input

s = sim()
s.calculate("income_tax", "2025-01")
c = s.clone()
c.set_input("income_tax", "2025-01", [7.0])
print(s._user_input_keys is c._user_input_keys)          # True

Suggested fix: in delete_arrays, drop the entries for the deleted variable, branches and periods; in clone, copy the set (set(self._user_input_keys)). A per-stored-array input flag copied with storage would also fix both.

PolicyEngine/policyengine-uk#2025 works around this in the UK Simulation subclass (clone and delete_arrays overrides), because income_support_eligible uses the record to decide whether an award was entered directly. Those overrides can go once core keeps the record in step.