Standardize Bash CLI entrypoints around .sh commands and per-command scripts

[codeforester]

Summary

This PR tightens the Bash CLI command conventions so the user-facing entrypoints and the command implementation layout are both explicit and self-identifying.

Bash commands now use .sh entrypoint symlinks in cli/bash/bin/, and command targets now resolve only from cli/bash/commands/<cli>/<cli>.sh. This removes the older main.sh-style ambiguity and makes the Bash side line up better with the planned Python CLI layout.

What Changed

• updated bash-wrapper to treat .sh as the public Bash command suffix
• changed wrapper dispatch to resolve commands only from:
  • cli/bash/commands/<cli>/<cli>.sh
• removed support for cli/bash/commands/<cli>/main.sh
• updated command listing to show Bash commands as *.sh
• renamed Bash entrypoint symlinks in cli/bash/bin/ to use .sh
  • for example, setup.sh instead of setup
• moved the setup command implementation to:
  • cli/bash/commands/setup/setup.sh
• updated wrapper, setup, and stdlib tests to match the new convention
• updated Bash CLI docs to reflect the new entrypoint and target naming rules

Why

This gives us a cleaner long-term separation between Bash and Python command surfaces:

• Bash commands are visibly Bash commands at the entrypoint layer: setup.sh
• Python commands can stay extensionless later without colliding conceptually with Bash commands
• command implementation files are easier to identify in search results, stack traces, and reviews
• the repo no longer accumulates many unrelated main.sh files with different responsibilities

Verification

Validated with:

bats cli/env/tests/banyanenv.bats \
     cli/bash/bin/tests/bash-wrapper.bats \
     cli/bash/commands/setup/tests/setup.bats \
     cli/bash/lib/std/tests/lib_std.bats