Release v2.5.0

• new feature: pestifer make-ligand-mol2 subcommand that, given a 4-letter RCSB PDB code or a path to a local .pdb file, generates a CGenFF-ready Tripos mol2 file for every HETATM ligand whose resname is not already defined in the loaded CHARMM topologies; for each unknown ligand it fetches the SMILES from the RCSB Chemical Component Dictionary (preferring the OpenEye canonical-stereo descriptor), builds an RDKit Mol whose heavy atoms are in PDB order and carry the original PDB atom names, protonates at the target pH (default 7.4) via Dimorphite-DL, places explicit Hs in 3D, and writes the mol2 via Open Babel with --title <RESNAME> so the CGenFF binary/web tool registers the resulting RESI under the correct residue name (rather than the leaked tempfile path); per-ligand failures are surfaced in a summary table without aborting the run, and --smiles RESNAME=... overrides the RCSB lookup when a custom tautomer or charge state is needed
• new feature: new pestifer.charmmff.ligand_paramgen subpackage exposes the building blocks reused by make-ligand-mol2 as a library: fetch_ligand_smiles(comp_id) (RCSB lookup with LRU caching and HTTP-error → RCSBLookupError mapping), protonate_ligand(residue, smiles, ph) (RDKit + Dimorphite-DL pipeline that preserves PDB heavy-atom order and stamps each heavy atom with the original PDB name on the _pdb_name property), write_mol2(mol, resname, outpath) (PDB-block-via-obabel writer that propagates _pdb_name and assigns sequential H1, H2, ... names to hydrogens), and generate_ligand_mol2s(parsed, charmmff_content, outdir, ph, smiles_overrides) (the orchestrator the subcommand calls, which the build workflow will also call for unknown ligands)
• new feature: well-known per-user toppar cache at ~/.pestifer/toppar/; when this directory exists, pestifer automatically prepends it to charmmff.user_custom.searchpath so .str files dropped there are picked up by every build without requiring a user_custom block in YAML; any project-local searchpath entry is loaded after the cache and overrides it (last-loaded wins) with a warning naming both files; designed as the default destination for .str files produced by running make-ligand-mol2 output through the CGenFF binary or web tool
• enhancement: charmmff.user_custom.searchpath entries now expand ~/ (the user's home directory) and shell environment-variable references like $HOME/foo or ${SCRATCH}/charmm before the directory check; previously those were taken literally and silently failed
• behavior change: CHARMMFFContent.add_custom_directory no longer asserts on duplicate-basename clashes between searchpath entries; instead, the later-loaded file wins and a warning is emitted naming both paths (the assertion previously crashed pestifer when, e.g., the user's project happened to contain a .str file with the same basename as one in the cache); same-resname clashes across differently-named files in the searchpath also emit a warning and follow last-loaded-wins semantics, so a project-local override of a cached parameterization is surfaced without silently merging
• new optional dep: [project.optional-dependencies] table in pyproject.toml declares an ligand-paramgen extra (pip install 'pestifer[ligand-paramgen]') that pulls in rdkit and dimorphite_dl; the obabel binary remains a runtime-PATH dependency, documented alongside the new subcommand
• test: tests/unit/test_charmmff/test_charmmffcontent.py::TestCharmmffContent.setUpClass was picking the CHARMMFF version directory by mtime rather than by parsed month-year (the production ResourceManager.charmmff_version_dirs() orders semantically); when the feb26 and jul24 directories were extracted out of release order, mtime selected jul24 and the test's hard-coded counts (calibrated against feb26) failed by ~1400 residues; setUpClass now delegates to ResourceManager.charmmff_version_dirs() so the test always exercises the same CHARMMFF release that production code uses
• test: new tests/unit/test_charmmff/ligand_paramgen/ package covers the ligand-paramgen building blocks (29 tests): protonation invariants on five SMILES across a pH=7.4 charge range, RCSB descriptor-priority selection under unittest.mock of requests.get, mol2 title/atom-name round-trip via the real obabel binary, and orchestrator-level altloc dedup and known-resname filtering using real Hetatm objects; test_charmmffcontent.py gains three TestAddCustomDirectory cases (tilde expansion, duplicate-basename warning + last-wins, duplicate-RESI warning + last-wins) that build a stub CHARMMFFContent via __new__ to avoid paying the full tarball-load cost
• doc: new docs/source/subs/make-ligand-mol2.rst covers the subcommand with examples (PDB code, local file, SMILES override, pH override) and outlines the CGenFF round-trip workflow (web tool → ~/.pestifer/toppar/); linked from the subcommand toctree in usage.rst; the charmmff.user_custom schema docstring gains "Per-user toppar cache" and tilde-expansion sections