Fix MCP dep tool parameter names to match CLI (issue_id/depends_on_id)

- Changed from confusing from_id/to_id to clear issue_id/depends_on_id
- Matches CLI convention: bd dep add [issue-id] [depends-on-id]
- Updated all tests and implementations
- Fixes GH #113 where Claude Code was creating dependencies backwards

Closes bd-58

Amp-Thread-ID: https://ampcode.com/threads/T-f01aca11-a10f-4908-9ce6-7e1734f2068f
Co-authored-by: Amp <amp@ampcode.com>

integrations/beads-mcp/src/beads_mcp/server.py

@@ -386,15 +386,15 @@ related (soft link), parent-child (epic/subtask), discovered-from (found during
 )
 @require_context
 async def add_dependency(
-    from_id: str,
-    to_id: str,
+    issue_id: str,
+    depends_on_id: str,
     dep_type: DependencyType = "blocks",
     workspace_root: str | None = None,
 ) -> str:
     """Add a dependency relationship between two issues."""
     return await beads_add_dependency(
-        from_id=from_id,
-        to_id=to_id,
+        issue_id=issue_id,
+        depends_on_id=depends_on_id,
         dep_type=dep_type,
     )