fix: Fix API pre-workflow hook execution order and enable auto-discovery

[WebOfNakedFancies]

what

• Modified /api/plan and /api/apply endpoints to run pre-workflow hooks before building commands instead of after
• Added support for auto-discovery when both Projects and Paths fields are empty in API requests
• Aligned API execution order with the comment flow architecture to ensure consistent behavior
• Fixed issue where dynamically generated atlantis.yaml files (via pre-workflow hooks) could not be used with the API

why

• The API had a critical chicken-and-egg problem: it tried to load atlantis.yaml before pre-workflow hooks could generate it
• This caused "cannot specify a project name unless an atlantis.yaml file exists" errors for repos using dynamic config generation
• The API flow was architecturally inconsistent with the comment flow (which runs hooks early and works correctly)
• Without auto-discovery support, API users couldn't replicate atlantis plan (no args) behavior
• Repo-level workflow configurations were being ignored when using the API, defaulting to server-defined workflows instead of project-specified ones (e.g., custom terragrunt workflow)

Execution Order Before Fix:
API: Clone → Load Config ❌ → Build Commands → Run Pre-Hooks (too late) Comment: Clone → Run Pre-Hooks ✅ → Load Config → Build Commands

Execution Order After Fix:
API: Clone → Run Pre-Hooks ✅ → Load Config → Build Commands Comment: Clone → Run Pre-Hooks ✅ → Load Config → Build Commands

tests

• Tested with dynamically generated atlantis.yaml via pre-workflow hooks - config now generates before being read
• Verified API requests with Projects: ["dev"] properly resolve project configurations and apply repo-level workflows
• Confirmed auto-discovery works when Projects and Paths are omitted from API request
• Validated backward compatibility - existing API calls with explicit Projects/Paths continue to work
• Verified logs show correct workflow merging: "overriding server-defined workflow with repo-specified workflow"