t-0hmura/mlmm_toolkit: mlmm-toolkit v0.2.5

Changes

• ml_hessian_mode unified into hessian_calc_mode
• RFO trust_radius 0.30→0.10, trust_max 0.30→0.20
• IRC: --hess-device, --read-hess; freq: --dump-hess (Hessian reuse)
• tsopt/all: --skip-final-freq
• Auto-shorten absolute paths and suppress consecutive blank lines in CLI output

Fixes

• IRC bisection: fix in-place mutation corrupting displacement arrays
• IRC initial displacement clamp 0.5→3.0 au
• all: --preopt default corrected to True
• extract: --exclude-backbone default changed to False
• path_search: fix missing MLMM_CALC_KW import
• dft.py: fix tmp.cleanup() → tmpdir.cleanup()

Docs

• fix defaults, YAML keys, and tables across EN/JA docs
• Fix dark mode toggle (3-state → 2-state)