Bug: No Entry Points added when re-installing plugin

[micahpw]

When re-installing a plugin, the cli doesn't add the entrypoints again, forcing the user to clear the cache.

To reproduce:

1. Install plugin X
2. Remove Plugin X
3. Install Plugin X again

micahwebb@Amys-MBP r2x-cli % cargo run install https://github.com/NREL/r2x-reeds --branch ml/move-plugins
Finished dev profile [unoptimized + debuginfo] target(s) in 0.06s
Running target/debug/r2x install 'https://github.com/NREL/r2x-reeds' --branch ml/move-plugins
Installed 7 entry point(s) in 5338ms

• r2x-reeds==0.0.1
  micahwebb@Amys-MBP r2x-cli % cargo run install https://github.com/NREL/r2x-reeds --branch ml/move-plugins
  Finished dev profile [unoptimized + debuginfo] target(s) in 0.07s
  Running target/debug/r2x install 'https://github.com/NREL/r2x-reeds' --branch ml/move-plugins
  Audited 1 package in 9ms
  micahwebb@Amys-MBP r2x-cli % cargo run remove r2x-reeds
  Finished dev profile [unoptimized + debuginfo] target(s) in 0.07s
  Running target/debug/r2x remove r2x-reeds
  Uninstalled 7 plugins(s)

• r2x-reeds
  micahwebb@Amys-MBP r2x-cli % cargo run install https://github.com/NREL/r2x-reeds --branch ml/move-plugins
  Finished dev profile [unoptimized + debuginfo] target(s) in 0.07s
  Running target/debug/r2x install 'https://github.com/NREL/r2x-reeds' --branch ml/move-plugins
  ⠴ Installing: https://github.com/NREL/r2x-reeds warning: No plugins found in package 'https://github.com/NREL/r2x-reeds'
  Installed 0 entry point(s) in 394ms

• r2x-reeds==0.0.1

[micahpw]

Also, after removing the plugin, the "list" command shows the following message instead of the helpful message to use "r2x install" to install a package. (This would only apply if you removed all the plugins.)

micahwebb@Amys-MBP r2x-cli % cargo run list
Finished dev profile [unoptimized + debuginfo] target(s) in 0.07s
Running target/debug/r2x list
Plugins:
Total plugin packages: 0

[micahpw]

This is still broken or is a misleading user experience in r2x-v0.0.16. The command r2x clean --yes works but removing individual plugins doesn't full remove the plugin from the manifest. Re-installing the plugin leads to warnings an entry points are no longer discovered.

Reproduction steps:

mwebb@mwebb-43264s r2x-cli % r2x clean --yes
Removed 16 plugin(s)
mwebb@mwebb-43264s r2x-cli % r2x list
There are no current plugins installed.

To install a plugin, run:
r2x install
mwebb@mwebb-43264s r2x-cli % r2x install r2x-reeds
Using Python 3.12.12 environment at: /Users/mwebb/.config/r2x/.venv
Audited 1 package in 7ms

• r2x-reeds==0.3.1
  mwebb@mwebb-43264s r2x-cli % r2x remove r2x-reeds
  Uninstalled 8 plugins(s)

• r2x-reeds
  mwebb@mwebb-43264s r2x-cli % r2x list
  Plugins:
  r2x-reeds:

Total plugin packages: 1
mwebb@mwebb-43264s r2x-cli % r2x install r2x-reeds
Using Python 3.12.12 environment at: /Users/mwebb/.config/r2x/.venv
Resolved 30 packages in 1.34s
Prepared 1 package in 82ms
Installed 1 package in 2ms

• r2x-reeds==0.3.2
  warning: No plugins found in package 'r2x-reeds'
• r2x-reeds==0.3.2
  mwebb@mwebb-43264s r2x-cli % r2x list
  Plugins:
  r2x-reeds:

Total plugin packages: 1

[micahpw]

Running r2x sync after uninstalling and re-installing a plugin will re-discover the plugins. However, it should be rediscovered just by running r2x install [plugin]