fix: write molecular_clock.txt in clock command

[ivan-aksamentov]

fix: write molecular_clock.txt in clock command

• Resolves: clock does not create a text-file with the rate estimate #574

The treetime clock command prints the rate estimate to stdout but never saves it to a file, despite the documentation listing "a text-file with the rate estimate" among the output files. The timetree command already writes this file via inline code.

Extract a shared save_molecular_clock() helper [src] that writes molecular_clock.txt and prints a confirmation message. Use it in both estimate_clock_model() [src] and run_timetree() [src], replacing the duplicated inline file-writing code.

The run_timetree print message for molecular_clock.txt incorrectly said "Inferred sequence evolution model" -- a copy-paste from the GTR block directly above it. The shared helper now prints a consistent --- molecular clock model (saved as ...) message for both commands.

Verification

Before (clock command produces no molecular_clock.txt):

$ treetime clock --tree data/h3n2_na/h3n2_na_20.nwk --dates data/h3n2_na/h3n2_na_20.metadata.csv --sequence-len 1400 --outdir clock_results
$ ls clock_results/
outliers.tsv  rerooted.newick  root_to_tip_regression.pdf  rtt.csv

After:

$ treetime clock --tree data/h3n2_na/h3n2_na_20.nwk --dates data/h3n2_na/h3n2_na_20.metadata.csv --sequence-len 1400 --outdir clock_results
--- molecular clock model (saved as clock_results/molecular_clock.txt):

Root-Tip-Regression:
 --rate:	2.826e-03
 --r^2:  	0.98
$ ls clock_results/
molecular_clock.txt  outliers.tsv  rerooted.newick  root_to_tip_regression.pdf  rtt.csv
$ cat clock_results/molecular_clock.txt
Root-Tip-Regression:
 --rate:	2.826e-03
 --r^2:  	0.98

Work items

• Add molecular_clock.txt output to estimate_clock_model()
• Extract shared save_molecular_clock() helper to deduplicate file-writing between clock and timetree
• Fix copy-paste "Inferred sequence evolution model" message in run_timetree() for the molecular clock file

Possible improvements

• Align print style for sequence_evolution_model.txt saves in run_timetree [src] and ancestral_reconstruction [src] to use --- prefix (both use '\nInferred ...' while all other file-save messages use '--- ...')