fix(config): don't conceal a previous override with the base settings

[Conaclos]

Summary

Fix #3176

When we convert the Biome Configuration to Workspace settings, we use the base settings to set the missing settings in every override. This results in overrides that conceal previous overrides.

For example, the following config:

  {
    "linter": {
      "rules": {
        "suspicious": { "noDebugger": "off" }
      }
    },
    "overrides": [
      {
        "include": ["index.js"],
        "linter": {
          "rules": {
            "suspicious": { "noDebugger": "warn" }
          }
        }
      }, {
        "include": ["index.js"]
      }
    ]
  }

was resolved to:

  {
    "linter": {
      "rules": {
        "suspicious": { "noDebugger": "off" }
      }
    },
    "overrides": [
      {
        "include": ["index.js"],
        "linter": {
          "rules": {
            "suspicious": { "noDebugger": "warn" }
          }
        }
      }, {
        "include": ["index.js"],
        "linter": {
          "rules": {
            "suspicious": { "noDebugger": "off" }
          }
        }
      }
    ]
  }

The current PR fixes the issue by removing the propagation of the base configuration to every override.

I also fixed several erroneous implementations.
For example, we took the first override.{linter.formatter.organizeImports}.enabled into account, while we have to take the last one.

I think there are still some issues. Some fields such as jsx_runtime are not behind an Option in overrides.
This means that every overrides has a default value for this field.
This is a change for a future PR.

Test Plan

I added new tests to avoid any regressions.

[Sec-ant]

Sorry I tried to rebase and update the snapshots, but I forgot to accept them before commiting them. 🥺

Fixed

[ematipico]

Damn, I will never understand overrides, my brain just fails to get them 😓