fix: migrate to new Jira /search/jql API endpoints for Cloud only

[clx-jlmoreno]

Description

Resolves the Jira search API deprecation issue by migrating to the new /search/jql endpoints for Cloud only.

Fixes #658 - Addresses the deprecation of /rest/api/2|3/search endpoints (effective August 1st, 2025).

Solution Implementation

Following the official Adaptavist migration guide, this PR implements Cloud-only migration:

✅ Cloud vs Server/DC Differentiation

• Cloud: Uses new POST /rest/api/3/search/jql endpoint
• Server/DC: Continues using existing /rest/api/*/search endpoints
• Detection: Based on config.is_cloud setting

✅ API Migration (Cloud Only)

• Old: GET/POST /rest/api/2|3/search
• New: POST /rest/api/3/search/jql
• Payload: Changed from query params to JSON body

✅ Pagination Update (Cloud Only)

• Cloud: nextPageToken with isLast flag
• Server/DC: Continues using startAt parameter

✅ Response Format Handling (Cloud Only)

• Default: Issue IDs only (["PROJ-123", "PROJ-124"])
• With fields: Full issue objects (backward compatible)
• Auto-detection: Handles both formats seamlessly

✅ Server/DC Compatibility Maintained

• No breaking changes for Server/DC installations
• Identical behavior as before for on-premise deployments
• MCP contract preserved across all deployment types

Files Changed

• src/mcp_atlassian/jira/search.py - Cloud/Server differentiation logic
• src/mcp_atlassian/models/jira/search.py - Response parsing for both formats
• src/mcp_atlassian/models/jira/issue.py - ADF description handling
• tests/unit/jira/test_search.py - Updated for both Cloud/Server scenarios

Testing

✅ Live Environment Tested

• Jira Cloud: crealogixme.atlassian.net
• Project: ARQBE
• Epic: ARQBE-11
• Issue: ARQBE-525

✅ Unit Test Coverage

• 383 Jira tests pass
• 24 search-specific tests pass
• Both Cloud and Server/DC paths tested

Impact

• Zero breaking changes for existing users
• Server/DC: Continues working exactly as before
• Cloud: Future-proof until August 1st, 2025 deadline
• Performance: Improved pagination for Cloud
• Compatibility: Works with both Cloud and Server/DC

[clx-jlmoreno]

Update: Squashed commits into a single clean commit for easier review.

✅ Changes consolidated:

• Main Jira Cloud API migration fix
• Code formatting and linting compliance fixes
• Single commit with comprehensive message

The PR is now ready for review with a clean git history! 🚀

[eciuca]

We need someone to review and merge this, please!

[michaelper22]

Would be very excited to see either this or #731 merged 🙏

[ChadNedzlek]

Same. The MCP is completely broken for me without this...