Remove simulate_tree() and simulate_tree_from_pop() and replace usage with simulate_chains()

[jamesmbaazam]

This PR closes #181 by:

• Unexporting and removing all occurrences of simulate_tree() and simulate_tree_from_pop(),
• Replacing their use with simulate_chains() in tests, vignettes, and examples.

Additionally, where necessary, descriptions involving simulate_tree() and simulate_tree_from_pop() have been rephrased. Examples include the README (64015e1) and Getting Started vignettes (e38453a).

[github-actions]

This pull request:

• Adds 0 new dependencies (direct and indirect)
• Adds 0 new system dependencies
• Removes 2 existing dependencies (direct and indirect)
• Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (26748ba) 99.26% compared to head (bbdb332) 99.41%.

❗ Current head bbdb332 differs from pull request most recent head 173ef46. Consider uploading reports for the commit 173ef46 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #182      +/-   ##
==========================================
+ Coverage   99.26%   99.41%   +0.15%     
==========================================
  Files           8        8              
  Lines         682      517     -165     
==========================================
- Hits          677      514     -163     
+ Misses          5        3       -2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[sbfnk]

LGTM

[sbfnk]

Also closes #158

[jamesmbaazam]

Thanks. #158 will be better addressed by #186.

[sbfnk]

Ah sorry yes that makes sense