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Skill configuration overrides ignored at runtime despite being parsed and logged

Skill configuration overrides ignored at runtime despite being parsed and logged: a task in LegoFlow-SWE (Harbor dataset). The skill system configuration overrides are being parsed and logged but silently discarded at runtime. When agent builders configure values like checkpoint every n: 10 or…

The task

The skill system configuration overrides are being parsed and logged but silently discarded at runtime. When agent builders configure values like `checkpoint_every_n: 10` or `warn_at_usage_ratio: 0.4` in their `default_skills` config, those values should affect behavior but currently do nothing.

Part of Lego-X/LegoFlow-SWE.