JTPRO: A Joint Tool-Prompt Reflective Optimization Framework for Language Agents

LLM tool agents can be improved without retraining by modifying the runtime harness around a fixed model: prompts, tool interfaces, middleware, state handling, and recovery logic. We study this setting as resource-bounded harness selection for fixed-model multi-turn tool agents, with the search surface scoped to prompts and tool-boundary middleware: edits are guarded intercepts at the tool boundary, not arbitrary rewriting of agent execution logic. Our optimizer-agnostic protocol reports mean held-out lift, worst-condition lift, repeatability, logged cost diagnostics, and RelLift95(B), a conservative estimate of the held-out gain of the harness selected under budget B. We instantiate the protocol with prompt-only and prompt-plus-middleware optimizers, including PRISM, which clusters failures and routes repairs to prompt, tool-boundary middleware, or joint edit surfaces within a Pareto search. On BFCL multi-round, tau2-Retail, and tau2-Telecom, PRISM obtains mean held-out lifts of 14.2, 14.9, and 10.1 percentage points and positive empirical RelLift95 on all three benchmarks, and a component ablation attributes the margin chiefly to failure-surface routing and the edit-pattern constraint. Across optimizers, the results show that some search procedures can occasionally find large gains but still choose brittle updates, so the reliability of the chosen harness should be reported alongside average held-out lift.

Large language model (LLM) agents increasingly interleave natural language reasoning with external tools such as web search and code execution. These tool-use policies are often optimized via reinforcement learning (RL), which can amplify spurious correlations in the training data. In this work, we study when and why RL-trained agents learn shortcut tool-selection policies: invoking tools based on superficial prompt cues rather than genuine task requirements. We construct controlled synthetic environments combining factual question answering and mathematical reasoning tasks, and inject cues that are strongly correlated with specific tools during training but causally irrelevant to tool necessity. Across counterfactual evaluations where cues are present but the associated tools are not required, agents exhibit substantial shortcut behavior, with spurious tool invocation rates increasing by up to 39 percent. However, shortcut formation is not universal: across the conditions we test, it arises only when the agent has already learned to use the target tool reliably, suggesting that task competence, rather than dataset imbalance alone, is a key factor in shortcut learning. A swapped-cue analysis further shows that semantic alignment between cues and tools substantially amplifies this effect. To mitigate these failures, we introduce a dense, decision-level reward in which an LLM judge evaluates the necessity of each tool call. This tool-necessity reward effectively suppresses cue-driven tool use while preserving task performance, providing a practical approach to improving the robustness of LLM agent tool-use policies.

Tool-augmented reasoning has become a popular direction for LLM-based agents, and it is widely assumed to improve reasoning and reliability. However, we demonstrate that this consensus does not always hold: in the presence of semantic distractors, tool-augmented reasoning does not necessarily outperform native CoT. To explain this performance gap, we propose a Factorized Intervention Framework that isolates the cost of prompt formatting, the overhead of the tool-calling protocol, and the actual gain from executing tools. Our analysis reveals a critical tradeoff: under semantic noise, the gains from tools often fail to offset the "tool-use tax", which is the performance degradation introduced by the tool-calling protocol itself. To address this, we introduce G-STEP, a lightweight inference-time gate to mitigate protocol-induced errors. While this yields partial recovery, our findings suggest that more substantial improvements still require strengthening the model's intrinsic reasoning and tool-interaction capabilities.