refactor(cli): use individual Command instances instead of global program

[mirceanis]

What issue is this PR fixing

This PR refactors the way commander.js is used in the CLI package.
Instead of a global program command being mutated by different imports, each subcommand is created as an independent instance of a Command object.

The main purpose is to simplify testing, however due to incompatibilities between jest/ESM/chalk/typeorm the tests can't actually be performed using the same testing harness.

A custom jest config would be needed that must only be used on the CLI tests. When enabling the workaround in jestjs/jest#12270 (comment) any tests using typeorm in any way will fail.
This means we'd also need to only use JSON storage or memory storage configs in these CLI tests.

This PR also exports some of the methods used to configure the CLI through yaml.

Quality

Check all that apply:

• I want these changes to be integrated
• I successfully ran pnpm i, pnpm build, pnpm test, pnpm test:browser locally.
• I allow my PR to be updated by the reviewers (to speed up the review process).
• I added unit tests... but they are skipped for now.
• I added integration tests.

[codecov]

Codecov Report

Base: 80.25% // Head: 85.45% // Increases project coverage by +5.20% 🎉

Coverage data is based on head (941693a) compared to base (125bf42).
Patch coverage: 83.82% of modified lines in pull request are covered.

❗ Current head 941693a differs from pull request most recent head 85041ef. Consider uploading reports for the commit 85041ef to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             next    #1130      +/-   ##
==========================================
+ Coverage   80.25%   85.45%   +5.20%     
==========================================
  Files         118      145      +27     
  Lines        4056    14906   +10850     
  Branches      875     1561     +686     
==========================================
+ Hits         3255    12738    +9483     
- Misses        798     2168    +1370     
+ Partials        3        0       -3     

Impacted Files	Coverage Δ
packages/core-types/src/coreEvents.ts	100.00% <ø> (ø)
...s/credential-ld/src/module-types/jsonld/index.d.ts	0.00% <0.00%> (ø)
packages/data-store-json/src/types.ts	0.00% <0.00%> (ø)
packages/did-comm/src/didcomm.ts	83.26% <ø> (+10.12%)	⬆️
packages/did-comm/src/index.ts	100.00% <ø> (ø)
packages/did-comm/src/message-handler.ts	72.10% <ø> (+12.64%)	⬆️
.../protocols/coordinate-mediation-message-handler.ts	89.63% <ø> (ø)
packages/did-comm/src/protocols/index.ts	100.00% <ø> (ø)
...omm/src/protocols/messagepickup-message-handler.ts	91.25% <ø> (ø)
.../did-comm/src/protocols/routing-message-handler.ts	89.65% <ø> (ø)
... and 209 more

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