fix: harden edge-case handling and clean up packaging

[gp201]

Bump version to 1.2.1 and bundle a set of robustness fixes, packaging cleanup, and a CI guard against version drift.

Robustness fixes:

• cli: use shlex.split() for --usher-args so quoted/escaped args parse correctly
• utils: abort with a clear error when the reference FASTA has != 1 record
• utils: handle PermissionError (non-executable binary) in run_subprocess_command
• utils: extract mutation position via regex in sortFun instead of string slicing
• ref_muts: abort when no samples match the alignment instead of failing on an empty root sequence; simplify consensus derivation and empty-mutation handling
• plot_barcode: drop unparseable positions and skip the plot when nothing remains
• generate_barcodes: dedupe clades by index (keep last) instead of full-row dedup
• format_tree: strip all whitespace when reading the newick line
• auspice_tree_to_table: default cumulative_branch_length so child recursion is safe; exclude "name" from attributes to avoid a duplicate 'name' column

Packaging / CI:

• pyproject: drop unused deps (pathlib, six, numpy)
• MANIFEST.in: drop conda build files and missing assets dir
• add scripts/check_version_consistency.py and a CI job to keep pyproject.toml and init.py versions in sync