LLM agents must select tools from large API libraries and order them correctly. Existing methods use semantic similarity for both retrieval and ordering, but ordering depends on inter-tool data dependencies that are absent from tool descriptions. As a result, semantic-only methods can produce negative Kendall-$τ$ in structured workflow domains. We introduce SkillGraph, a directed weighted execution-transition graph mined from 49,831 successful LLM agent trajectories, which encodes workflow-precedence regularities as a reusable graph foundation prior. Building on this graph foundation prior, we propose a two-stage decoupled framework: GS-Hybrid retrieval for candidate selection and a learned pairwise reranker for ordering. On ToolBench (9,965 test instances; ~16,000 tools), the method reaches Set-F1 = 0.271 and Kendall-$τ$ = 0.096; on API-Bank, Kendall-$τ$ improves from -0.433 to +0.613. Under identical Stage-1 inputs, the learned reranker also outperforms LLaMA-3.1-8B Stage-2 rerankers.