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/tests/test_mcp_server_integration.py

@@ -382,7 +382,7 @@ async def test_add_dependency_tool(mcp_client):
     # Add dependency
     result = await mcp_client.call_tool(
         "dep",
-        {"from_id": issue1["id"], "to_id": issue2["id"], "dep_type": "blocks"},
+        {"issue_id": issue1["id"], "depends_on_id": issue2["id"], "dep_type": "blocks"},
     )
 
     message = result.content[0].text
@@ -523,7 +523,7 @@ async def test_dependency_types(mcp_client):
     # Test related dependency
     result = await mcp_client.call_tool(
         "dep",
-        {"from_id": issue1["id"], "to_id": issue2["id"], "dep_type": "related"},
+        {"issue_id": issue1["id"], "depends_on_id": issue2["id"], "dep_type": "related"},
     )
 
     message = result.content[0].text