codacy_cli_analyze does not honor usesConfigurationFile — regenerates flat config and reports false positives (ESLint) #84

Summary

When a tool is configured to "use the repository configuration file"
(usesConfigurationFile: true), the MCP's codacy_cli_analyze still
regenerates the Codacy pattern-catalog config and analyzes against it,
ignoring the repo's config file. This produces false positives.

Environment

• OS: macOS
• IDE: VS Code + Copilot (Agent mode)
• Tool affected: ESLint 8.57.0
• Repo config file: .eslintrc.json (on default branch, main)
• Codacy UI: ESLint → "Use configuration file" is ENABLED
• API confirms: codacy_list_repository_tools returns ESLint with
  "hasConfigurationFile": true, "usesConfigurationFile": true

Expected

The CLI should skip generating .codacy/tools-configs/eslint.config.mjs
and run ESLint against .eslintrc.json.

Actual

codacy_cli_analyze regenerates eslint.config.mjs from the pattern
catalog (with no-undef: ["error"], no Mocha/WebdriverIO globals) and
reports no-undef false positives for describe, it, before,
driver, etc. — errors that do not exist under the repo's .eslintrc.json.

Root cause

Running the CLI directly reproduces both behaviors:

• WITHOUT init flags (how the MCP invokes it):
  codacy-cli analyze --tool eslint <file>
  → prints "ESLint configuration created based on Codacy settings"
  → regenerates eslint.config.mjs → reports no-undef false positives

• WITH init flags:
  codacy-cli analyze --tool eslint --api-token $TOKEN --provider gh --organization <org> --repository <repo> <file>
  → prints "Skipping config generation for ESLint - configured to use
  repo's config file"
  → uses .eslintrc.json → 0 false positives

In src/cli/MacCodacyCli.ts, analyze() calls:
${cli} analyze ${file} --format sarif (with only { tool })
It does NOT forward --api-token / --provider / --organization / --repository, so codacy-cli analyze cannot fetch usesConfigurationFile
and falls back to regenerating the flat config.

Suggested fix

Have analyze() forward the same init params that initialize() already
builds (api-token, provider, organization, repository) to the
analyze command, so the CLI can honor usesConfigurationFile.

Note

init alone is not sufficient — analyze re-evaluates
usesConfigurationFile from its own flags and regenerates the config
when they're absent, even after a correct init.