Model Context Protocol

Machine-learning libraries such as Weka and scikit-learn were designed for human programmers. Language-model agents now use these same libraries by recalling APIs from memory and writing code, an approach that hides what a library offers, delays errors until runtime, and loses experimental state between turns. We present TuiML, a self-contained machine-learning library built for AI agents, with native algorithms across supervised, unsupervised, time-series, data handling, tuning, and evaluation tasks. Every component describes itself through machine-readable metadata and parameter schemas, so an agent can search the library, inspect components, compose validated workflows, and register new ones that become discoverable in turn. Every call is validated, seeded, and traced, and sessions export as runnable notebooks, making experiments reproducible by construction. One specification layer drives the Model Context Protocol (MCP), agent-framework adapters, a Python API, a CLI, and local model serving, while data and models never leave the machine. Benchmarks show TuiML remains predictively competitive with scikit-learn and Weka. While looking like a conventional library to a human user, TuiML is designed for agents first, allowing them to read, extend, and operate machine learning autonomously. TuiML is open source, with documentation at https://tuiml.ai.

AI agents increasingly execute long-running workflows that externalize effects through independently supplied tools. Under retries, speculative execution, concurrency, and partial failures, the resulting external state may be inconsistent with the workflow's intended resolution: required effects may be missing or duplicated, aborted effects may survive, and committed effects may depend on provisional state that is later withdrawn. Advanced transaction models address related failures, but assume that lower-level operations expose the semantics they depend on: whether an effect occurred, whether it can be compensated, staged, or safely reordered. Shared agent-tool interfaces usually do not. We contribute an effect-history model that separates events in the external world from the runtime's observations of them, and a catalog of eight recurring external-effect anomalies. From the catalog we derive the boundary capabilities required to exclude each anomaly in general, and four points where black-box tool invocation alone cannot provide a general guarantee. We then ask how much of this is expressible in a widely used shared tool interface, measuring the use of the standard annotation vocabulary across 98,291 tools exposed by registered Model Context Protocol (MCP) servers. The fields are widely emitted but provide only coarse call-level hints, and none of the required capabilities is fully expressible. These results motivate reusable transactional contracts at the tool boundary.

Multi-tenant tools commonly accept a tenant identifier and validate it against the caller's entitlement. For a large language model (LLM) agent, that pattern delegates resource selection to a process whose context may contain attacker controlled instructions. We formalize this stochastic deputy problem and present a structural defense: remove tenant identity from the Model Context Protocol (MCP) tool schema, bind scope to a verified credential, and enforce it below the agent. In a 373-trial ablation across eight model configurations and two transports, a correctly validated tenant parameter served every out-of-scope attempt: 26 of 26, or 26 of 41 plausible-pretext trials overall. With the parameter removed, no tool signature could express the read. Twelve of 56 trials instead escaped the interface by forging writable scope, showing that interface invariance requires cryptographically protected context. On a production dataset containing multiple GBs of data, set-valued scope caused a measured $57\times$ latency ratio under function-wrapped membership predicates; a JSON_TABLE lateral join recovered index access where the tenant key was indexed. The evaluation also exposes deployment limits, including an entitlement-size query-planner cliff and incomplete index coverage. The result is a tenant-isolation argument that depends on enforceable interfaces and credentials rather than model compliance.

Studies of the Model Context Protocol (MCP) server ecosystem draw their samples in ways that quietly select for servers that work: reference sets, popularity lists, hand-curated frames, or pipelines that repair a server until it starts. We report what an unrepaired probability sample actually contains. From a 24,135-server registry census we draw 400 npm/stdio servers with a published seed and probe each one over the wire. Only 48.8% complete an initialize handshake, against 66.7% for a hand-curated frame measured with the same instrument, and the dominant failure is not missing credentials (13.3%) but servers that never start at all (37.5%). Among the 195 that do run, hard conformance is total: zero fatal JSON Schema violations across 2,766 advertised tools. Optional safety annotations are the real variance, and the tool-level omission rate on a random draw is 58.8% against 41.5% on the curated frame, so curation flatters this figure too. We then compare the tool descriptions these servers advertise against two tool-use benchmark corpora using one method held constant. Real MCP tools show 2.8% near-duplication at cosine 0.70, and all of it lies within single servers: cross-author near-duplication is 0.0% at every threshold tested. BFCL v4 shows 16.7%, of which 16.4 points lie between independently presented tasks. UltraTool shows 0.3%, cleaner than real tools, so this is a property of BFCL and not of synthetic corpora as a class. Separately, 68.8% of raw BFCL rows and 85.6% of raw UltraTool rows are exact name-plus-description repeats, against 0.4% for real MCP, so any statistic computed over these releases without global deduplication measures repetition rather than tools. All figures regenerate from released scripts and a published seed.

Conventional vulnerability analysis relies on either system access or dynamic interaction, all of which may be unavailable to third-party analysts auditing closed-source, remotely hosted, critical in situ systems, or commercially gated software. Therefore, we propose a new paradigm of no-box vulnerability analysis in which neither access nor runtime interaction is available, and only functionality metadata is available. Such metadata defines the intended behavior of the system, including its inputs, outputs, and side effects, while constraining the space of implementations consistent with that behavior. We propose hypothesizing about vulnerabilities that exist across all possible implementations of a given system metadata, without observing or interacting with the target system. An analyst can later validate these hypotheses when additional access is available. We showcase the feasibility of no-box vulnerability analysis through implementing a prototype called MCPSEC, which audits Model Context Protocol (MCP) servers for indirect prompt injection vulnerabilities using only the tool metadata exposed at server registration time. We evaluate MCPSEC on 20 widely deployed MCP servers comprising 177 tools, among which human evaluators confirm 95 vulnerable tools. MCPSEC identified 143 tools as vulnerable, and for each vulnerable tool, it produced a hypothesized vulnerability along with exploitation technique. Using metadata alone, MCPSEC predicted 94 (98.9% recall) real verified vulnerabilities, compared against an LLM baseline with 80 (84.2% recall). Overall, our results introduce no-box vulnerability analysis as a new analysis paradigm and demonstrate its practical feasibility in realistic systems.

Resource constrained single-board computers including Raspberry Pi, NVIDIA Jetson Nano, Arduino UNO Q, Orange Pi, and LattePanda motivate on-device small language model (SLM) agents that reduce cloud dependence, improve data locality, and tolerate intermittent connectivity. Model Context Protocol (MCP)-style tool invocation demands more than fluent generation: an agent must emit machine-readable JSON, select the correct tool, supply all required arguments, and avoid unintended actions. We establish a platform-agnostic CPU baseline by evaluating five open-weight models below two billion parameters Phi-1.5, Pythia-1.4B, TinyLlama-1.1B-Chat, Qwen2.5-0.5B, and Qwen2.5-1.5B on 100 prompts spanning weather retrieval, web search, calculation, email composition, and task creation, under greedy decoding and nucleus sampling. A recovery parser strips Markdown fences, extracts brace-delimited substrings, and scores parseability, tool-name correctness, argument completeness, and value agreement. Under this criterion, Qwen2.5-1.5B achieves 75% (greedy) and 79% (sampling); Qwen2.5-0.5B achieves 72% (greedy) but drops to 32% under sampling. Phi-1.5 scores 0%; Pythia and TinyLlama reach at most 7%. A strict post-hoc audit finds only 5 of 1,000 raw responses directly parseable as JSON, exposing near-total dependence on output recovery. A CPU resource probe shows Qwen2.5-1.5B requires 7,960 MiB and 30.782 s mean latency; Qwen2.5-0.5B uses 3,637 MiB and 10.627 s, revealing a reliability-resource trade-off for edge deployment. These results do not cover the named boards directly or a full MCP implementation. Safe deployment requires schema validation, constrained generation, least-privilege execution, and human escalation for consequential actions.

Large Language Models (LLMs) are increasingly employed to orchestrate robot behavior through natural-language interfaces, yet no benchmark exists to evaluate their reliability as safety-aware decision makers in human-humanoid collaboration. Unlike deterministic safety systems that enforce binary allow/deny decisions, LLM-based orchestrators exhibit a compliance spectrum ranging from overcompliance (refusing safe actions) to full safety violations. This paper introduces the first safety benchmarking environment for LLM orchestrators in human-humanoid collaboration, built on a Model Context Protocol (MCP)-based architecture with safety invariants grounded in ISO 10218-2:2025 protective measures. The benchmark defines five testable safety invariants, a four-level compliance taxonomy (correct compliance, overcompliance, undercompliance, full violation), and a three-layer evaluation pipeline (text prompting, simulated sensor-actuator loops, and physical validation on a Unitree G1 EDU humanoid). We report Layer-1 results: three cloud backends (Claude Haiku 4.5, GPT-4o-mini, Gemini 2.5 Flash) and a local open-weights baseline (qwen3:8b) across 40 100-turn sessions under full-context and sliding-window budget conditions, while the simulation and physical layers remain ongoing. We find that (1) model family determines the safety floor, as Claude and Gemini remain at or near zero violations while GPT-4o-mini commits up to 13 per session, (2) context management dissociates two failure axes, reducing mean behavioral issues by 42-57% for every cloud backend while nearly doubling GPT-4o-mini's violations (3.8 to 7.2 per session), and (3) proportional compliance, clamping movement speed to the rule-specified maximum rather than refusing, emerges consistently only in Gemini; the preliminary simulation layer reproduces the model ranking and the GPT-4o-mini failure-mode inversion.

Safety properties assessed separately for Model Context Protocol (MCP) tool use and Agent2Agent (A2A) delegation need not describe behavior when one agent uses both. We measure one such behavior in a single controlled MCP-to-A2A configuration: a testbed drives a real-model host across a local MCP and a local A2A leg into an ordered event trace scored by exact deterministic rules (no LLM judge), one restricted decision per trial. In a pre-specified, frozen three-arm design, each of 10 record scenarios appears with a CONFIDENTIAL header, with no header, and with PUBLIC - OK TO SHARE; the six substantive record values are byte-identical across arms, and the outcome is verbatim occurrence of any of them in the outbound message. Four models x 3 arms x 4 repeats give 480 trials; the scenario is the unit of generalization, and we report the 10 scenario-level values (mean, median, sign counts), with no p-values or intervals. The confidential-minus-unlabeled contrast is inconclusive and floor-limited in every model (both arms at or near zero), so it does not show that confidential labels lack a protective effect. Adding PUBLIC - OK TO SHARE is descriptively associated with higher verbatim egress relative to the unlabeled baseline, with strong model dependence: strong and consistent for Claude Sonnet 5 (public-minus-unlabeled mean +0.800, all 10 scenarios; mostly an association with whether Claude relays at all), moderate but floor-limited for one GPT-5.6 tier, small (median 0) for another, and a complete floor for the third. This is an association in one configuration, not a causal or general effect. Code, byte-pinned traces, and the offline analysis pipeline are released as a public artifact.

Orchestra composes two independently built bioinformatics MCP servers -- RegNetAgents, which infers gene regulatory network topology from ARACNe networks, and CASCADE, which supplies four independent evidence sources (LINCS knockdown, DepMap essentiality, super-enhancer status, DoRothEA transcription-factor confidence) -- into one multi-agent workflow exposed via the Model Context Protocol. Its central architectural claim is that requiring RegNetAgents' topology evidence and CASCADE's experimental evidence to agree on a candidate regulator yields a more trustworthy candidate than either alone -- not previously tested directly, since RegNetAgents' own validation asked only whether its candidate lists beat chance. We test this on the TCGA tumor-acquired regulator tier (regulators in a gene's tumor ARACNe network but absent from the GREmLN population-averaged baseline), selecting candidates by ARACNe mutual-information (MI) edge weight. On RegNetAgents' published BRCA/COAD focal-gene panel plus matched negative controls, agreement among at least 2 of the 4 CASCADE sources predicts OncoKB cancer-gene status among focal genes (odds ratio 2.89, Benjamini-Hochberg-adjusted p=0.0166) but not among negative controls (p=0.0721); a single source is not diagnostic for either group. The pattern replicates and strengthens in a third cancer type, STAD, on a separately constructed panel (odds ratio 5.82), and against an independently curated ground truth (the Sanger COSMIC Cancer Gene Census). MI edge weight is the strongest single predictor overall (p=0.0003); a logistic-regression likelihood-ratio test confirms corroboration adds value beyond it in both panels (p=0.0234; p=0.0001). Every experiment invokes Orchestra's real agentic entry point.

The Model Context Protocol (MCP) has become the de-facto interface for connecting LLM agents to enterprise tools, and adoption has been explosive: within a year, large organizations went from zero to dozens of internally built MCP servers. That speed created a governance crisis. Each team implemented authentication independently -- some with no auth, some with API keys, some with full OAuth -- producing a fragmented landscape with no consistent way to authorize callers, track who did what, or offboard a departing employee across the fleet. This paper reports an industry deployment that resolves the crisis with a centralized MCP gateway: a single aggregation, governance, and authentication layer that fronts every downstream MCP server. We make four contributions grounded in production experience. First, a two-axis authentication model crossing persona (interactive user vs. automated non-user) with credential type (no-auth, static/dynamic API key, PKCE, client credentials, platform app-context). Second, a gateway authentication layer supporting three enterprise SSO grants and three token-provisioning models: Bring-Your-Own-Token, Generate-Your-Own-Token, and delegated OAuth via RFC 8693 token exchange. Third, three end-to-end identity flows -- User-to-OAuth2, Non-user-to-Service-Account, and User-to-Service-Account -- composing client, gateway, and server. Fourth, the deployment evolution from CDN/WAF/edge perimeter to private MCP tunnels and enterprise-wide connectors. The architecture is in production, fronting dozens of MCP servers across web, desktop, custom-SDK, and low-code clients.

How much an AI coding agent costs to run can depend more on the agent scaffolding that drives it than on the interface through which it reaches its tools. We set out to measure the cost of tool use over the Model Context Protocol (MCP) against tool use over an ordinary command-line interface (CLI), a difference on which published estimates disagree by more than an order of magnitude while resting on practitioner reports that cannot be reproduced. We ran one fixed software task -- six operations against a private online git repository -- across seven agent scaffoldings and five language models, and we verified completion by inspecting the repository state rather than trusting the agent's self-report. The dominant effect was the scaffolding. Two of the seven ship no MCP support at all; they completed every run using only the CLI, which shows that MCP is unnecessary for this class of work, and they were 5.0x to 28x cheaper than the five scaffoldings that do support MCP, comparing CLI runs alone with no MCP server attached anywhere. The effect was largest for a small 27-billion-parameter model running locally, whose cost varied 139x across scaffoldings while it completed the task under all of them. The comparison we set out to make proved unstable: thirteen strictly paired MCP-to-CLI ratios span 0.43x to 29x, with outliers on both sides. The two interfaces separate on the cost of failure, where 12.9 per cent of the money spent on MCP runs bought no completed work against 2.2 per cent on CLI runs, but not on its frequency: failures were equally common in both, in the original runs and in their repetitions alike. Agents frequently ignored the interface they were assigned, so comparisons that do not verify actual behaviour measure an unknown mixture. The harness, the task, the verification and the complete dataset are released as open source.

The Model Context Protocol (MCP) standardizes how servers expose data and tools to Large Language Models (LLMs). A common server design embeds frequently used reference data, such as identifier lookup tables, directly in the server instructions: the system-prompt text a server hands to the host application. When a query concerns an entry of the embedded table, the model can act on it immediately instead of re-discovering the same information through a search tool. We test whether client LLMs actually consume such instruction-embedded data, reporting a 54,000-trial study across 24 LLMs (9 Claude, 6 Gemini, 9 GPT) on a production legal-information MCP server. A diagnostic condition that removes the competing search tool shows that failures are dominated by behavioral preference rather than missing capability. With search unavailable, 23 of 24 models read the embedded data reliably (hit ratio at least 98%); with a search tool merely present, 9 models drop below 15%. A 2^3 factorial analysis of three instruction-level interventions reveals strong interaction effects: combining all three restores at least 86% for 20 of 24 models, but individual interventions can backfire for specific model families. Per-server prompt engineering is therefore a workaround rather than a fix; we argue that MCP host applications should provide an explicit mechanism that places server instructions ahead of tool selection in the client LLM's deliberation.

EDA scripting with tool-specific, often undocumented APIs remains a long-tail bottleneck that existing LLMs fail to address. This paper presents ZhuLong, an execution-grounded LLM coding agent for PyAether and SKILL that combines API retrieval, documentation inspection, and sandbox execution via unified MCP tools, augmented by an offline API self-exploration mechanism that infers undocumented API behaviors through counterfactual experimentation. We evaluate ZhuLong on EDA-Eval-PyAether, a benchmark of 158 real-world tasks with assertion-based execution, where the complete system achieves 78.5% Pass@1 in the commercial Empyrean Aether environment, substantially outperforming a pure LLM baseline (23.6%). Ablation studies identify sandbox execution as the dominant performance driver (41.2 pp drop when removed), with the self-exploration mechanism contributing an additional 3.2 pp accuracy gain and a 22.1% reduction in per-task tool calls. On 20 interactive tasks involving unsaved layouts and schematics, ZhuLong achieves 60.0% Pass@1 for PyAether and 50.0% for SKILL.

Agent evaluations tell us that a model picked the wrong tool, but rarely why. We introduce canary tools: diagnostic probe tools planted in an agent's Model Context Protocol (MCP) tool set, each engineered to probe one specific tool-selection weakness. A six-type taxonomy (semantic decoys, parameter traps, capability mirages, prerequisite blindness, temporal decoys, and granularity traps) turns a single "wrong tool" outcome into a multi-dimensional profile of how a model reasons about tools. We evaluate eight models -- six hosted and two 8B open-weight -- spanning three capability tiers, on 120 tasks across three canary-density conditions and three seeds (8,640 runs), plus a 2,880-run subtlety ablation. Task success is graded by a provider-independent judge, corroborated by a second independent judge (Cohen's kappa = 0.75). We report three findings. First, susceptibility drops sharply as models get more capable: the per-task canary susceptibility rate (CSR) ranges about 36x across models, lowest for Claude Opus 4.8 and highest for Llama 3.1 8B. Second, capability tier alone does not predict safety: the most susceptible hosted model is mid-tier, and within a provider the cheaper model can be the safer one. Third, the taxonomy is capability-stratified: capability mirages most reliably trap frontier models, while the other types are largely inert on strong models but fire on small open models, so they discriminate by capability rather than being weak. Softening each canary's give-away phrase leaves frontier CSR essentially unchanged, evidence that the probes measure reasoning, not phrase-spotting. Susceptibility also predicts task failure (Spearman rho = -0.34), while the most robust models are not significantly degraded by canary pressure. We release the framework, canary schemas, tasks, and logs.

The Model Context Protocol (MCP) has seen rapid adoption since its November 2024 launch, with over 21,000 server instances detectable on the public internet. We present the first dynamic behavioral security assessment of internet-facing MCP servers, combining passive discovery across eleven data sources (crt.sh, HuggingFace, GitHub, npm, Smithery, PyPI, Censys, FOFA, Shodan, glama.ai, and pulsemcp.com) with active dynamic testing using Corvus, a purpose-built framework implementing 34 test modules covering 10 MCP-specific vulnerability classes. Across four measurement runs spanning July 2026, we confirm 640 production MCP servers and dynamically audit 414, uncovering 68 reportable vulnerabilities including SQL injection, SSRF targeting cloud metadata services, prompt template injection, and path traversal via cursor manipulation. We find that 91.8% of dynamically audited servers lack OAuth authentication, 687 tool instances across confirmed servers expose shell execution capabilities without access controls, and 41.6% of confirmed servers disappear within three days between consecutive measurement runs---indicating rapid deployment cycles without security review. We report on our responsible disclosure pipeline and release Corvus as an open-source framework for MCP security evaluation.

Language-model agents are increasingly deployed under standing instructions: a system prompt, a policy file, or a skills document is placed in context, and the agent is trusted to let that document govern every action that follows. Existing benchmarks rarely test this deployment pattern directly; they measure whether an agent can complete a task, not whether a long, binding policy document constrains its behavior over an extended tool-use horizon. We present HANDBOOK_md, a benchmark of 65 agentic tasks modeled on how employees follow company handbooks. Each task places an agent in a self-contained company environment (a file workspace with mock email, chat, calendar, issue-tracking, and commerce services exposed over the Model Context Protocol) and instructs it to carry out routine professional work governed by an expert-written standard operating procedure of 20-124 pages. Tasks span five domains (finance, medical billing, insurance, logistics, and HR) and 10 fictional companies. To resist memorization, every task modifies one of 10 base handbooks, altering the specific rules and thresholds on which grading depends, so no two tasks share the same set of policies. Grading is fully deterministic: each task carries a rubric of programmatic criteria (824 in total) that check both that required actions occurred and that prohibited actions did not. Under strict grading, where a trial passes only if every criterion is satisfied, the strongest evaluated model passes 36.2% of trials, and most frontier models remain below 25%. Failures follow consistent patterns: agents let a plausible but unauthorized in-environment request override the standing policy, perform a required check and then act against its result, lose rule details over long horizons, and report compliance they did not achieve. We release the tasks, environments, and evaluation harness.

The rapid development of large language model (LLM) agents has enabled their broad adoption across diverse real-world tasks. To standardize interactions between LLM agents and external environments, Model Context Protocol (MCP) tools have emerged as a de facto standard and have been widely integrated into these systems. However, the use of MCP tools also introduces new safety risks, as LLM agents can be induced to perform malicious or unauthorized actions. Although prior work has proposed defenses for securing tool use in LLM agents, most methods rely on static analysis, i.e., inspecting prompts and generated outputs, which limits the defense effectiveness and robustness. To address these limitations, we propose MTGuard, a hybrid analysis-based defense framework designed to safeguard the use of MCP tools in LLM agents by leveraging lifecycle-aware static-dynamic co-analysis. Extensive evaluation demonstrates that MTGuard effectively mitigates multiple categories of harmful tool use across different LLM agents while maintaining performance on benign user tasks.

Recent industry practice has seen the rapid emergence of agentic systems composed of heterogeneous, tool- and LLM-mediated agent components, raising practical questions about inter-agent coordination and protocol design. This paper presents an implementation-grounded comparison of the Model Context Protocol (MCP) and the Agent2Agent (A2A) protocol, from a multi-agent systems engineering perspective, using an inter-agent coordination scenario involving LLM-based agents. We evaluate an MCP-based and an A2A-based multi-agent implementation of the same software engineering task against a set of requirements derived from prior literature and discussions with industry partners, including agent discoverability, multi-part messaging, multi-turn conversations, asynchronous communication, observability, interoperability, and access control. The results evidence that MCP can support inter-agent coordination in constrained LLM-based systems through a comparatively lightweight implementation model with lower coordination complexity, although coordination concerns such as conversational state management and task lifecycle handling must be implemented explicitly at the application layer. In contrast, A2A provides richer native support for stateful, multi-turn coordination through protocol-level abstractions for tasks and lifecycle management, but this comes with substantially greater implementation and coordination complexity. Given the narrow scope of the evaluated coordination pattern, these findings are presented as design observations from an empirical experience report rather than general claims of protocol suitability or superiority across broader classes of MAS, highlighting trade-offs and how protocol abstractions shape the distribution of coordination responsibilities in contemporary agentic systems.

Large Language Models (LLMs) excel at natural language understanding and generation but remain unreliable for multi-step logical reasoning, especially in safety-critical or compliance-sensitive domains. Recent neuro-symbolic approaches address this gap by coupling neural models with external symbolic engines, yet most integrations are bespoke and lack a standardized interface for tool-augmented agents. This paper presents Euclid-MCP, an open-source MCP server that provides deterministic logical reasoning via SWI-Prolog. Euclid-MCP introduces Euclid-IR, an engine-agnostic intermediate representation for Horn-clause logic that is human-readable, easy for LLMs to generate, and straightforward to compile into Prolog or alternative backends. The server exposes a compact tool interface that supports a translate-run-inspect-repair loop, enabling LLM clients to delegate inference while retaining full access to proof traces and derivation logs. We evaluate Euclid-MCP on a realistic IT security and compliance use case. Results show that while LLMs alone are sufficient on small knowledge bases, they hallucinate systematically on larger problems, whereas Euclid-MCP delivers exact answers with lower latency and more compact outputs. We argue that semantic RAG is fundamentally unsuited for rule enforcement, and that Euclid-MCP can serve as a stable, shared reasoning substrate for both RAG-based assistants and agentic systems.

The Model Context Protocol (MCP) is an open-source standard that allows AI agents to connect to external tools, databases, and services. While this connectivity enables powerful agent capabilities, it also introduces multi-step attacks that existing per-call defenses cannot reliably detect. Attackers can compose individually benign tool invocations into malicious sequences that evade isolated inspection. This paper presents ChainWatch, a sequential detection framework for identifying multi-step attacks in MCP-based AI agent systems. ChainWatch models attack progression using a six-stage kill chain and applies a Hidden Markov Model (HMM) to classify tool-call sequences. Detection rules are triggered when a session exhibits suspicious progression across multiple stages. The framework is supported by a structured threat model covering direct sequential attacks, indirect prompt injection chains, and hybrid multi-stage attacks. A 20-dimensional feature extraction schema captures behavioral signals from tool interactions. We demonstrate the approach using five representative attack scenarios from the security literature, showing how ChainWatch detects attack chains that evade traditional per-call security mechanisms.

Large language models (LLMs) are increasingly used to automate data-processing workflows, yet coding agents typically produce scripts that are not automatically materialized as persistent, editable platform artifacts. We call this disconnect the \textit{NL2Pipeline gap}. To bridge it, we introduce \textsc{DataFlow-Harness}, a platform that guides an LLM agent to construct platform-native directed acyclic graphs (DAGs) through typed, incremental mutations rather than free-form scripts. The platform combines \textsc{DataFlow-Skills} for procedural guidance, a Model Context Protocol (MCP) layer that exposes the live operator registry and current pipeline state, and \textsc{DataFlow-WebUI}, which synchronizes conversational authoring with a visual DAG editor. On a 12-task data-engineering benchmark, \textsc{DataFlow-Harness} achieves a 93.3% observed end-to-end pass rate. Relative to Vanilla Claude Code, it reduces measured monetary cost by 72.5% and generation latency by 49.9%; its observed pass rate is within 0.9 percentage points of the Context-Aware Claude Code baseline while its cost is 42.8% lower. Per-task analysis indicates that Skills are most useful when construction depends on implicit procedural knowledge. These results show that live platform grounding can produce persistent, editable workflow artifacts with an observed reliability close to script-generation baselines and with lower measured construction cost and latency.

LLM agents increasingly rely on tool calling to act on external systems, and the Model Context Protocol (MCP) has quickly become its de facto interface. Operating MCP at cloud scale, however, becomes difficult. On the tool provider side, legacy services are not directly callable through MCP; the rapid protocol development also creates ongoing compatibility cost. On the agent side, the number of accessible tool is limited by the LLM context window and inference overhead; mounting a large tool set increases token usage and inference latency and can reduce task success rate. Moreover, for stateful MCP backends with multiple replicas, preserving session affinity increases client-side complexity. We present a cloud-scale gateway system for MCP service. It breaks the direct-connect model on the data plane and offloads legacy service integration, consolidating incompatible MCP variants, access control, tool recommendation, and session-aware routing to the gateway. Hybrid retrieval sustains 98% Top-15 recall; it scales agent tool access to 3,000+ with high tool selection accuracy, and reduces tool selection time by $8.9\times$ and token usage by $23.8\times$, with low per-call overhead, stable under scale-out. Finally, we share the lessons learned from deploying the gateway system in production.

As Model Context Protocol (MCP) servers emerge as the core infrastructure for connecting LLMs with external tools, existing benchmarks leverage real-world MCP servers to evaluate LLM agents' tool-using capabilities. However, these benchmarks overlook the continuous evolution of tool interfaces and functionalities within MCP servers, resulting in flawed assessments that fail to capture the agent's adaptability in changing tool landscapes. To bridge this gap, we introduce \textbf{MCPEvol-Bench}, a novel benchmark for evaluating the task-solving capabilities of LLM agents under dynamic toolset evolution. Inspired by large-scale empirical study, we propose 11 mutation operators to simulate realistic tool evolution within 123 MCP servers. We benchmark 12 state-of-the-art LLMs on multiple versions of MCP servers, revealing that even frontier models struggle to adapt to evolving tools. For instance, GPT-5.4 and Claude-Sonnet-4-6 exhibit performance declines of 13.7% and 14.4% in evolved MCP servers, respectively, accompanied by substantial increases in planning and reasoning errors. These findings highlight the vulnerability of LLM-driven workflows, establishing MCPEvol-Bench as a standard for evaluating agent adaptability in dynamic tool environments.

Tool-using LLM agents are mostly evaluated assuming all tools work. When a tool times out, returns a week-stale value, or has its description poisoned in deployment, the developer needs a controlled way to reproduce the failure, test a fix, and confirm the fix worked before deployment. We present AgentCheck, an open-source web workbench that turns an MCP server into an intervention surface. AgentCheck runs an agent against its real tools and records every tool response, then re-runs the agent with the response perturbed by a fault (12 types) injector. Matching tool calls are replayed from cache, and later tool calls go live after the agent diverges. This yields a reproduce-intervene-confirm loop: the developer toggles a mitigation, re-runs against the identical fault, and sees if the failure goes away. Scoring has two parts: deterministic pass/fail rules, plus an LLM judge for interpretive labels, validated against human annotations. Across five agents, the best passes 105/120 scenarios and the weakest only 77. The failures are usually silent, confident use of incorrect tool outputs rather than crashes. On the weakest agent, a retry mitigation raises success on timeout error faults from as few as 30% of cases to 100%, whereas stale-data faults remain near 3-4 of 10 regardless of the mitigation. AgentCheck makes these failure modes reproducible, comparable, and verifiable before deployment.

Modern coding agents expose multiple tool surfaces -- IDE primitives, bash, and Model Context Protocol (MCP) code-execution -- and the field has shipped three contradictory claims about which one matters. We run the missing crossed comparison: an integrity-clean three-arm ablation (baseline / bash_only / code_only) on synthetic computation tasks and SWE-bench Mini modification tasks, holding model, harness, and prompts fixed, with two agents (Claude Code, OpenAI Codex CLI) so the comparison spans both regime and agent-design axes. Across the four resulting (regime, agent) cells, restricting the agent to a single execute_code MCP tool is cheaper than -- or statistically tied with -- its cheapest tool-rich rival in three cells (significantly on Artifact/Claude and SWE-bench/Codex; directionally on Artifact/Codex), with pass rates statistically tied within each cell. The lone exception is SWE-bench/Claude, where code_only is directionally costlier (+14.4%, not significant); a conditional-cost analysis localizes that gap to failure-cost on doomed-run trajectories, not a per-edit tax on successful runs. Two implications: the cheapest tool surface is jointly determined by task regime and agent design rather than by either axis alone, and the headline cost signal lives in cache-adjusted cost -- not pass rate, which is invariant across surfaces at the model sizes we evaluate. The benchmark harness, task suite, and analysis code are available at https://github.com/hyang0129/onlycodes.

The rapid emergence of the Model Context Protocol (MCP) has introduced a new standard for connecting large language models to external tools and services. Despite its rapid adoption in open-source development, systematic understanding of how MCP is implemented, structured, and maintained remains limited. This study presents the first large-scale, evidence-based dataset of real-world MCP implementation collected directly from GitHub. Using a hybrid pipeline that integrates the GitHub REST and GraphQL APIs with custom Python verification scripts, 3,238 candidate repositories were discovered, filtered, and validated through multi-stage evidence checks. Each verified project was classified by operational role (e.g., client, server, gateway) and exported in a reproducible JSONL schema. A manual review of a representative subset confirmed an overall precision of 83% at a 95% confidence level, and additionally revealed a set of repositories functioning primarily as educational samples, tutorials, or demonstration templates. A targeted exclusion rule was then applied to remove these non-operational repositories, resulting in a final dataset of 2,297 validated MCP projects. The analysis shows that Python and TypeScript dominate MCP development, with hybrid architectures emerging as the most common design pattern. By emphasizing transparent verification strategies, structured evidence tagging, and reproducible data organization, this work establishes a foundational benchmark for studying real-world MCP ecosystems and supports future research on integration, connectivity, and compatibility across the broader developer community.

Large language model (LLM) agents are increasingly deployed over Model Context Protocol (MCP) servers, yet the benchmarks used to evaluate them score the final answer or a fixed "ground-truth" list of tools, both of which are fragile once the underlying data is live and stateful. We present DynamicMCPBench, a reusable framework rather than a fixed dataset. A practitioner can run it on their own MCP servers to test models on their own tasks, or let it collect servers automatically to measure a model's general ability to solve agentic tasks. Given the servers and any set of models, it generates realistic goals, pursues each one live to record a successful trajectory, distills that trajectory into path-agnostic effect checkpoints, and scores an agent on whether it reproduces those effects, never on the final answer. To show what the framework reveals, we run it at scale: 24 models over 121 servers and 750 tasks spread evenly over 15 task categories (50 each), where each category targets a distinct tool-use challenge of the generated questions. Each task is scored by pass^3: it counts as solved only if all three independent attempts succeed. Even the strongest agents solve only about half of the tasks, 31% of tasks are solved by no model at all, and accuracy collapses as the required tool chain grows longer (from 39% on the shortest chains to 13% on the longest). A human validation study confirms the automatic scoring is reliable (chance-corrected agreement of 0.76). DynamicMCPBench thus turns benchmark construction into something practitioners can rerun on their own servers and models, while exposing a consistent inability of current agents to handle long, multi-step agentic tasks.

The Model Context Protocol (MCP) is the dominant way coding agents discover and invoke external tools. A server advertises each tool through a tools/list handshake that returns a name, a natural-language description, and a JSON input schema. The client renders this metadata once, in a one-time approval dialog, and then injects it verbatim into the model's context on every subsequent turn. Nothing in the protocol requires the rendered approval view and the bytes delivered to the model to match. We isolate that gap as a single structural mechanism, concealment encoding, and show with a model-free, protocol-free analysis that Unicode's TAG block (U+E0000 to U+E007F) has no assigned glyph in any mainstream terminal, chat, or IDE renderer, so a payload written in it is absent from what a human reviewer sees while surviving byte-for-byte into the model's tokenizer. We then measure whether this mechanism actually defeats today's client-side defenses, building a proof-of-concept that speaks the real MCP JSON-RPC/stdio protocol against a genuine client and server. Across 5 distinct MCP metadata surfaces we implement 8 concrete techniques with a deterministic, protocol-level harness. All 8/8 techniques deliver an attacker-controlled payload into the model's context, 4/8 evade a representative string-matching sanitizer, and exactly as the mechanism analysis predicts, only the TAG-block encoding (1/8) is invisible in the human approval view while still reaching the model verbatim. MCP forces re-approval for 0/8 techniques even under a time-of-check to time-of-use rug-pull. To test whether these outcomes are a property of the protocol or an artifact of one server codebase, we re-implement the catalogue against 3 independently developed Python MCP server libraries and find total agreement across all 32 cross-library outcome cells. The baseline sanitizer flags 0 of 25 benign descriptions.

Large language model agents driving security tool suites over the Model Context Protocol are increasingly common. Yet the factors that bound their capability remain poorly characterized: how much depends on the model versus the client that drives it, whether constraining the agent to the orchestrator's own tools helps, and where capability is limited by reasoning rather than by missing tools. Using HexStrikeAI, an open-source orchestrator that exposes 150+ tools, as a testbed, we follow a methodology that evaluates the system, diagnoses its failures, and applies targeted improvements. We run 86 picoCTF challenges across seven categories and three difficulty tiers, under three tool-access regimes and three model/client configurations (774 trials). We then apply corrections to existing tools, agent-behavior changes, and eleven new capability tools, and re-run the previously-unsuccessful trials. The diagnosis isolates the driving client as a first-order factor for a fixed model (a 2.1 * gap between two DeepSeek clients) and a monotonic difficulty gradient, with the largest gains in the mid tier. The overall solve rate rises from 55.4% to 72.0%, and every configuration improves significantly (paired McNemar p < 0.001, non-overlapping 95% confidence intervals). The residual failures are reasoning- or environment-bound rather than missing-tool. A 60-run stability sub-study finds single-run verdicts reproducible (17/20 unanimous). We discuss what the results imply for how such orchestrators should be evaluated, and we are explicit about the limits: the study uses a single benchmark, the fixes were tuned on the same challenges they were evaluated on, and the client effect is demonstrated for one model only, so its generality to other models remains a hypothesis.

Autonomous AI agents increasingly depend on external knowledge stores, yet most retrieval pipelines provide relevance without durable guarantees of provenance, version identity, integrity, traceability, or point-in-time reconstruction. We formalize this as context governance and present ContextNest, an open specification and reference implementation for governed AI-consumable knowledge vaults. ContextNest does not replace Retrieval-Augmented Generation (RAG); it supplies the governance layer beneath retrieval, determining which artifacts are approved, current, attributable, and integrity-verified before retrieval systems operate over them. The specification combines typed Markdown documents with metadata, deterministic set-algebraic selectors, contextnest:// URI references, SHA-256 hash-chained version histories, graph-level checkpoints, source nodes for live data through the Model Context Protocol (MCP), and audit traces of agent context consumption. These mechanisms let organizations reconstruct which knowledge versions informed an agent output and whether those versions were AI-eligible when consumed. We report first empirical results from two controlled experiments. In a stale-version attack isolating the governance-versus-retrieval failure mode, governed selection strictly Pareto-dominates BM25 sparse retrieval, with higher answer-quality pass rate (97% versus 93-90%) at about one-third the input-token cost. In a retrieval-determinism experiment over a 1,060-document corpus, deterministic selectors and BM25 return stable document sets across repeated identical queries (Jaccard 1.0), while a dense+HNSW baseline is non-deterministic on 80% of queries (mean Jaccard 0.611, worst case 0.210). These results suggest that context governance addresses failure modes retrieval quality alone is not designed to resolve. We release a core engine, CLI, and MCP server under open licenses.

Agent interoperability protocols (MCP, A2A, ACP, ANP, and ERC-8004) have rapidly matured to enable identity, capability discovery, tool access, and message exchange between autonomous agents. However, as enterprises deploy heterogeneous agent fleets that must make collective decisions under governance constraints, a question arises: can these protocols support governed agent communities, or only task-oriented coordination? We present a systematic gap analysis applying a six-dimension governance requirements taxonomy (membership, deliberation, voting, dissent preservation, human escalation, and audit/replay) derived from organizational theory, multi-agent systems literature, and enterprise governance standards. We analyze each protocol's specification against this taxonomy, classifying capabilities as Supported, Partial, or Absent. The resulting gap matrix reveals that voting and dissent preservation are universally absent across all five protocols, deliberation is absent or at most partial, and no protocol encodes the full set of primitives required for governed agent communities. We distinguish extensible gaps (addressable through protocol extension mechanisms) from structural gaps (requiring a new architectural layer) and assess time-sensitivity based on observed protocol evolution velocity. The analysis establishes that agent community governance constitutes a missing architectural layer above current interoperability standards, not a missing feature within them.

The Model Context Protocol (MCP), introduced by Anthropic in November 2024, defines a standardized interface for connecting large language models (LLMs) to external tools, data sources, and services. Within months of release, hundreds of community-built MCP servers appeared on GitHub, but no software-maintenance literature has yet described how the ecosystem is being structured in production. This industry experience paper catalogues five recurring MCP server architectural patterns observed across an enumerated corpus of fifteen independently developed servers (five production servers from the ANSYR voice AI platform plus ten public servers from the official MCP registry): Resource Gateway, Tool Orchestrator, Stateful Session Server, Proxy Aggregator, and Domain-Specific Adapter. Each pattern is described in the structured form of Gamma et al.: context, problem, solution, and consequences. We also document four anti-patterns and a set of cross-cutting concerns around authentication, versioning, and observability. The quantitative evaluation contributes three measurements: inter-rater reliability of the taxonomy across two independent LLM raters on 54 held-out servers (Cohen's kappa = 0.76), which also localizes three pattern-boundary ambiguities; transport overhead measured end-to-end on loopback and modeled for cross-host paths; and a tool-count study showing tool-selection accuracy drops below 90% between 10 and 15 tools per context for Claude Haiku 4.5 and between 20 and 30 tools for Sonnet 4. Code, corpus, and prompts are released as a replication package.

Model Context Protocol (MCP)-style ecosystems give language-model applications a practical connection layer for tools, resources, prompts, and transports. As agents move from connection to execution, security decisions often remain split across clients, servers, prompts, approval dialogs, OAuth deployments, and logs. This paper asks whether a runtime can make execution-layer invariants explicit and testable while preserving MCP-like workflows. We define eight invariants: metadata non-authority, grant-backed approval, canonical resources, principal binding, scoped capability invocation, source-and-target data-flow authorization, deny-path audit, and explicit protocol state. We implement these invariants in HCP, a Handle-Capability Protocol reference runtime for MCP-style agent execution that represents calls through principals, resources, grants, capabilities, handles, policy decisions, data-pipe checks, and audit entries. We evaluate HCP against two MCP-like baselines: a naive connection-layer runtime and a practice-informed connection-layer mitigation baseline with metadata linting, session checks, and per-call approvals. Across 10 benchmark cases, the naive baseline permits all modeled attacks, the mitigation baseline permits 6 of 10, and HCP blocks all 10 while preserving audit evidence. Ablations identify which runtime components block attacks and preserve forensic evidence. A local in-memory microbenchmark reports sub-millisecond mean latencies for measured policy, invocation, peek, and pipe operations. A bounded GitHub README-screening sample provides ecosystem signals, not vulnerability findings. The results support a narrow claim: MCP-style agent systems need an execution-control layer in addition to connection-layer conventions.

Large language models are increasingly capable of mathematical reasoning, but the proofs they generate are often unreliable and hard to verify. Interactive theorem provers such as Lean 4 address this by accepting only kernel-checked proofs; however, their reach is bounded by the formalized knowledge available. While Mathlib, a repository of formalized Lean 4 theorems that covers diverse mathematical areas, certain specialized areas remain underrepresented; notably, the domain of Combinatorics on Words (CoW). CoW studies sequences, exploring their properties such as periodicity, borders, conjugacy, and morphisms. As a result, specialized provers, trained on Mathlib-centered data, lack the lemmas to operate in CoW. We present two contributions. First, we introduce a Lean 4 formalization of CoW containing eight modules and \textbf{93} declarations of core definitions and foundational lemmas. Second, we present LAMP, a multi-agent framework that synthesizes kernel-verified Lean 4 proofs by providing explicit, structured domain knowledge at inference time through an ontology, rather than by fine-tuning a prover. LAMP coordinates a Planner, Builder, and Verifier with Model Context Protocol based access to a domain-specific CoW ontology. In a suite of 90 CoW theorems that span all eight modules and three difficulty levels, LAMP synthesizes verified proofs for 96.7% of theorems, substantially exceeding both an unscaffolded baseline and existing specialized provers. An ablation shows that removing LAMP's tool-grounded architecture or its Planner/Builder separation each cost roughly 12 percentage points, even with the backbone model held fixed.

With the rapid evolution of LLM-driven agents, Model Context Protocol (MCP), an open protocol bridging LLMs with external tools, has quickly become foundational to modern agent ecosystems. However, the expanding adoption of MCP has also introduced novel security concerns such as Tool Poisoning Attack (TPA), which exploit LLM-server interactions to inject malicious prompts. Existing poisoning schemes typically adopt a monolithic plaintext embedding paradigm, which fails to withstand manual inspection or automated detectors. Current research still lacks a systematic analysis on multi-tool poisoning, where multiple tools can be exploited cooperatively to disperse detection risk. In this paper, we introduce ShareLock, a multi-tool threshold poisoning framework that utilizes Shamir's threshold scheme to ensure exceptional stealth and fault tolerance. ShareLock distributes the malicious instruction as benign-looking secret shares across multiple tool descriptions, achieving both information-theoretic secrecy and attack robustness against moderate auditing. After a covert reconstruction trigger is planted during server update, the aggregated shares reconstruct the hidden instruction, resulting in critical breaches of system assets or private data. To evaluate the realistic threat of ShareLock, we constructed a comprehensive benchmark encompassing four multi-tool scenarios and conducted extensive experiments across mainstream LLMs on two distinct MCP clients. Our results demonstrate that ShareLock significantly outperforms existing single-tool poisoning strategies in tool description-based detection while maintaining an average attack success rate exceeding 90%.

Automated test generation for telecom software systems and networks has advanced significantly with the adoption of machine learning and rule-based approaches. However, most existing solutions generate static test suites against a snapshot of the system; as code, configurations, topologies, and key performance indicators (KPIs) evolve, these tests quickly become outdated or misaligned with the live system. There is currently no widely adopted solution that continuously detects fine-grained changes and selectively adapts only the affected tests without regenerating entire test suites. This paper presents a context-aware generative AI framework for automated telecom test script generation that treats testing as a continuously adapting process driven by the current state of the system rather than a static artifact. The central contribution is delta-conditioned test generation over a live knowledge graph: our approach employs a continuously updated knowledge graph (KG) as a single source of truth, a delta engine for fine-grained change detection, and a KG-guided generative AI agent, operating via the Model Context Protocol (MCP), to create, update, or retire test cases automatically. We further integrate Retrieval-Augmented Generation (RAG) to enrich reasoning with telecom-domain knowledge and historical artifacts. We demonstrate applicability across software-system and telecom-network use cases, including a Python-based KPI monitoring application managed in GitLab, and show how the framework reduces manual effort, improves test relevance, and accelerates test cycles.

Federated learning over medical images is a demanding workflow application. Each round fans out across parallel client jobs and converges on an aggregation step that feeds the next round. At scale this yields 101 sub-workflows and 2,679 jobs on GPUs at four sites, which takes an expert months to build, mostly on workflow mechanics rather than science. We ask how far AI assistance can automate such workflows. An LLM agent, grounded in a released plugin of Pegasus-specific skills, first produces a reviewable specification of checkable constraints and acceptance criteria, then generates the executable workflow. A validation loop repairs runtime failures, checks code against those constraints, and regenerates the implementation from the specification alone. We evaluate three LLM agents, report end-to-end runs on the FABRIC testbed, and show how conformance checking against the specification caught three silent errors that failure-driven debugging missed, including one that trained 1,700 jobs on random tensors.

Tool-using LLM agents increasingly use the Model Context Protocol (MCP) to answer from heterogeneous evidence sources, including search, APIs, databases, clinical records, and formulary tools. Standard factuality metrics usually test whether an answer is supported by pooled evidence, missing a provenance-sensitive failure mode: a claim may be supported somewhere while being attributed to the wrong source. We call this cross-source conflation. We introduce ProvenanceGuard, a source-aware verifier for MCP-grounded answers. It consumes captured MCP traces with stable tool IDs, source IDs, and raw outputs; decomposes answers into atomic claims; routes claims to source-specific evidence; checks support with NLI and a token-alignment proxy; compares stated attribution with the routed source; and returns per-claim verdicts plus an answer-level allow/block decision. Blocked answers can be repaired with retrieval-augmented answer revision and re-verified. We evaluate on 281 medical-domain MCP-agent traces. A 266-trace adjudicated subset yields 2,325 LLM-assisted claim labels split by trace; 361 held-out labels are human-verified. On the 40-trace held-out split, ProvenanceGuard achieves block F1 0.802 and source accuracy 0.858 over 260 source-eligible claims, outperforming source-blind baselines that do not emit claim-to-source IDs. On a harder multi-source benchmark it reaches block F1 0.846, while source-plus-relation accuracy drops to 0.229, showing that exact source ownership remains difficult with semantically close sources. Repair-and-reverify resolves all blocked answers in the full trace set, often via conservative fallback. In 50 controlled clinical conflation probes, ProvenanceGuard detects all injected attribution swaps with no retained wrong attribution. These results show that source attribution is an independent axis for factuality verification in MCP-based agents.

AI coding assistants now support a growing share of software work, from quick scripts to production applications. Yet these agents remain largely stateless: each new session re-reads project files, re-derives prior decisions, and - most costly - may repeat debugging attempts that already failed. Reconstructing this context can consume an estimated 5,000-20,000 tokens per session; the bottleneck is often not model capability but missing project memory. We present projectmem, an open-source, local-first memory and judgment layer for AI coding agents. projectmem records development as an append-only, plain-text event log of typed events - issues, attempts, fixes, decisions, and notes - and deterministically projects that log into compact, AI-readable summaries served through the Model Context Protocol (MCP). Beyond storage, projectmem adds a deterministic pre-action gate that warns an agent before it repeats a previously failed fix or edits a known-fragile file. We frame this as Memory-as-Governance: memory that does not merely answer the agent but acts on its next action. The system runs fully offline with no telemetry; its immutable log also serves as a provenance trail for reproducible, auditable AI-assisted development. projectmem ships as a three-dependency Python package (14 MCP tools, 19 CLI commands, 37 automated tests) and is evaluated through a two-month self-study across 10 projects comprising 207 logged events. Source code: https://github.com/riponcm/projectmem.

Large Language Models (LLMs) in multi-turn interactions maintain evolving context rather than generating isolated responses, making them vulnerable to prompt-injection and context-poisoning attacks in which locally plausible adversarial fragments gradually distort reasoning trajectories. Existing defenses mainly filter individual outputs and often ignore context evolution across turns, leaving long-horizon reasoning exposed. Although the Model Context Protocol (MCP) standardizes context exchange and tool invocation, it functions as a passive routing layer and does not enforce contextual stability. To address these limitations, we introduce the Game-Theoretic Secure Model Context Protocol (GT-MCP), a controller-driven multi-agent method that treats context management as a closed-loop dynamical process. GT-MCP coordinates three heterogeneous LLM agents and selects outputs through a trust function that jointly evaluates causal consistency against a validated context graph, semantic agreement among agents, and distributional drift over time. When instability is detected, a rollback-based self-healing mechanism restores the validated context and prevents unsupported fragments from propagating. Empirical evaluation over 500 interaction turns under an adaptive adversarial threat model shows that contextual drift remains bounded in 99.6% of turns, with recovery required in only 0.4%. Per-turn utility remains tightly concentrated, with median = -0.19, P05 = -0.72, and P95 = 0.30; severe degradation below -1 occurs in only 0.4% of cases, and no injection attempt succeeds at the controller level. Selected outputs maintain stable win rates above 98%, and computational overhead remains predictable, with latency per token = 1.63e-3 s.

Large language models deployed as autonomous agents for enterprise workflows face a key challenge: verbose tool responses from enterprise systems can cause context overflow, stale-state errors, and high inference cost. We study this problem in automated expense itemization in Microsoft Dynamics 365 Finance and Operations using Model Context Protocol tools. We evaluate four GPT-5 configurations on a 50-task hotel expense benchmark: no user model, full conversation history, context pruned to the last 5 tool call/response pairs, and pruning with automated summarization. Results are averaged across 5 independent runs, with the user model held constant for the context-engineering comparison. The no-user-model baseline achieves only 8.0% complete itemization. Full-context retention improves completion to 71.0%, but consumes 1,480,996 tokens and 14.56 hours per benchmark. Pruning to the last 5 tool calls improves completion to 79.0% while reducing token use to 535,274 and runtime to 5.39 hours. Adding summarization achieves the best result: 91.6% complete itemization and 99.64% average amount itemized, with 553,374 tokens and 5.79 hours. We further report confidence intervals, effect-size analysis, sensitivity over pruning and summary windows, failure analysis, results across five expense types grouped into three categories, and cross-model evidence with Claude Sonnet 4.5. These results show that, for this class of enterprise tool-use workflow, selective retention of recent tool interactions plus compact summarization can improve both reliability and efficiency compared with full-history retention.

As the Model Context Protocol (MCP) standardizes tool-calling for autonomous agents, it introduces a critical, unexamined attack surface: the error-handling loop. We hypothesize that tool error messages possess implicit authority, triggering corrective reasoning modes that bypass standard safety heuristics. We introduce VATS (Vulnerability Analysis of Tool Streams), a mutation-driven framework that systematically evolves adversarial payloads across seven structural and linguistic dimensions. Our evaluation across four frontier models, Gemini 3.1 Pro, GPT-5.5, GLM-5.1, and Qwen3-Coder, demonstrates that error-path injection triples the success rate of standard indirect prompt injection (IPI), achieving up to 100% compliance in controlled evaluations. We isolate structural positioning (sandwiching instructions within error context) as the most effective exploit vector across all tested models. While we find that production framework guardrails can mitigate these vulnerabilities, the inherent susceptibility of the model layer poses a systemic risk to bespoke agentic workflows.

Long-horizon LLM sessions outlive their context windows, and the standard mitigations - truncation, summarization, retrieval - share a structural flaw: they treat history as flat text, discarding precisely the content that makes a session resumable: decisions and their rationales, task status, and file modification history. We present TokenMizer, an open-source transparent proxy that maintains session history as a typed knowledge graph and, at context boundaries, replaces the raw transcript with a token-budgeted serialization of session state. The schema comprises 14 node types and 7 edge types under an 8-state lifecycle in which decisions can be superseded or explicitly invalidated; bitemporal validity intervals support time-travel queries; and first-class decision-transition records preserve why each decision replaced its predecessor (trigger, reason, evidence). Version 0.3.1 embeds this memory core in a production-shaped serving layer - SSE streaming, security middleware, nine provider adapters, a monitoring dashboard, graph exports (D3 JSON, self-contained interactive HTML, Obsidian Canvas) - and exposes checkpoint/resume to agents as Model Context Protocol tools. The evaluation is deliberately minimal and fully provenanced: three synthetic sessions, heuristic-only extraction, one plain-summary baseline, every value traceable to a single versioned results file. Graph extraction ties the baseline on task recall (75.6%) and exceeds it on decision recall (85.0% vs. 70.0%) and file recall (100% vs. 91.7%), with 201-302-token resume blocks extracted in 8.1-529.9 ms per session. At n=3 these results are directional; ceiling effects and baseline weaknesses are analyzed explicitly. Code, benchmark runner, and the exact results file are released under the MIT licence.

Enterprise agent systems increasingly need to connect large language models to private tools, internal knowledge, and Model Context Protocol (MCP) interfaces. In this setting, raw task capability is insufficient: organizations also require policy enforcement, tenant-scoped isolation, and execution that remains within explicit operational boundaries. We present Queen-Bee, a governed multi-agent architecture in which a Queen control plane retrieves capabilities, plans task-scoped execution, and compiles a structured BeeSpec that is executed by specialized Bee agents under constrained tool access. We implement a working prototype with tenant-scoped MCP connectors, audit-backed execution-time governance, retrieval-driven weak incubation, and multiple provisioning backends. We evaluate the system on 59 enterprise-style tasks spanning governance-sensitive requests, retrieval-driven provisioning, scoped local execution, and chemistry workflow integration. The retrieval-driven Queen-Bee variant achieves a task success rate of 0.964, zero governance failures, and substantially better scoped execution quality than both a static Queen-Bee baseline and a permissive single-agent baseline. We further show a multi-Bee chemistry workflow with explicit approval gating and a concrete top-3 shortlist grounded in real upstream evidence and screening artifacts. Additional comparisons with hybrid retrieval and LLM-guided provisioning show that richer provisioning backends are viable but do not outperform the lightweight structured retriever on the current small, highly structured capability registry. The results provide prototype-level systems evidence rather than a production deployment study, and suggest that enterprise agent platforms should be evaluated not only by capability, but also by governed provisioning, isolation behavior, scoped execution quality, and artifact-aware workflow coordination.

MCP (Model Context Protocol) enables LLMs (Large Language Models) to interact with external tools and data sources via a standardized protocol. Its rapid adoption in tool-augmented Artificial Intelligence (AI) workflows has introduced new reliability challenges, such as configuration parameters that are accepted but not enforced at runtime, leading to unintended default behavior, whose runtime fault characteristics remain empirically unexamined. We present the first empirical taxonomy of runtime faults in MCP servers. We manually analyzed 837 MCP-specific runtime fault threads from 473 actively maintained MCP server GitHub repositories and derived a taxonomy using a bottom-up open coding procedure. The taxonomy comprises 11 top-level categories and 27 subcategories (73 leaf fault types), covering recurrent failures across protocol interactions, tool invocations, schema enforcement, state management, model-provider integration, security validation, and timeouts or explicit cancellations of in-progress operations. To assess the taxonomy's external validity, we surveyed 55 MCP server developers. Respondents reported experiencing an average of 20 of the 27 fault subcategories, and no category remained unobserved. These results indicate that the taxonomy reflects widely observed runtime failures in MCP-based systems and shall assist AI software maintenance and evolution in the future.

The Model Context Protocol (MCP) has emerged as a critical standard empowering Large Language Models (LLMs) to utilize external tools. In this ecosystem, LLMs rely on natural language descriptions provided by MCP servers to select and execute functions. This interaction implicitly assumes that tool descriptions faithfully reflect their underlying implementations, while this assumption is not mandatorily verified in practice. As a result, MCP deployments may suffer from a problem named Description-Code Inconsistency (DCI), where a tool's description of its capabilities and security boundaries is not consistent with what the code actually does. In this paper, we present a comprehensive study of DCI in real-world MCP servers. We formally define the problem and propose a comprehensive taxonomy spanning functionality inconsistencies and undeclared side effects. Guided by this taxonomy, we develop DCIChecker, an automated framework that combines structure-aware static analysis with the Direct-Reverse-Arbitration prompting method to cross-validate tool descriptions against actual code implementations. We apply this framework to a large-scale dataset comprising 19,200 description-code pairs extracted from 2,214 real-world MCP servers. Our measurement reveals that DCI is widespread, with 9.93% of these pairs exhibiting inconsistencies. We further demonstrate that DCI creates a critical defense blind spot, facilitating varied risks from operational failures to stealthy malicious behaviors. Finally, we propose mitigation strategies to enforce semantic consistency and enhance the reliability of the emerging agentic ecosystem.

Biomedical agents promise to automate complex biological workflows, yet current systems face two fundamental bottlenecks: bioinformatics tools are highly heterogeneous in interfaces and execution environments, while agent planning still relies on flat prompt-retrieved tool descriptions. As biomedical software ecosystems grow, this coupling between tool coverage and context size leads to tool confusion, unstable planning, and inefficient execution. We introduce BioManus, an MCP-native biomedical agent built on graph-scaffolded planning over structured biological capabilities. BioManus first introduces the BioinfoMCP Compiler, which converts heterogeneous bioinformatics software into standardized MCP servers, yielding a large executable MCP ecosystem. It then organizes this ecosystem as a typed heterogeneous MCP graph over tools, operations, datatypes, and workflow stages. At inference time, BioManus retrieves compact task-specific subgraphs, synthesizes operation-level workflow scaffolds. This design decouples planning complexity from raw tool inventory size, achieving a context compression ratio of Theta(N / (h * m_bar)) under high-recall retrieval, where N is the total tool count, h is the workflow horizon, and m_bar (much smaller than N) is the average number of candidate tools per operation. Experiments on BioAgentBench and LAB-Bench show that BioManus improves execution accuracy, workflow validity, and context efficiency over advanced biomedical agent baselines. This work suggests a paradigm shift: scalable biomedical reasoning requires structured executable capability graphs rather than increasingly larger prompt-level tool retrieval.

Training LLMs to orchestrate multi-step tool calls is held back by three coupled obstacles: realistic stateful execution environments are costly to build, synthetic training queries are often detached from the server's actual state (so the generated tool calls fail to execute), and recall-based RL rewards incentivize verbose tool-calling patterns. We present PROVE (Programmatic Rewards On Verified Environments), a framework with three contributions: (1) a library of 20 stateful MCP (Model Context Protocol) servers exposing 343 tools, enabling live-execution RL training with session-scoped state isolation; (2) a state-machine data synthesis pipeline that generates multi-turn tool-call trajectories grounded in live-sampled server state, so generated queries reference entities that actually exist; and (3) a multi-component programmatic reward with an adaptive efficiency penalty that counters the verbosity incentive of recall-based rewards. We train four models (Qwen3-4B, Qwen3-8B, Qwen2.5-7B, Granite-4.1-8B) with GRPO on the resulting ~13K training examples. On BFCL Multi-Turn, tau2-bench, and T-Eval, PROVE yields improvements of up to +10.2, +6.8, and +6.5 points respectively, demonstrating that this framework yields consistent gains on multi-step tool orchestration across two model families.

Autonomous science is moving from demonstration to infrastructure. Large language model agents now plan experiments, and self-driving laboratories execute them. Yet every such system rebuilds the link between the reasoning agent and the physical instrument from scratch, against fragmented vendor SDKs and standards built for deterministic software clients rather than probabilistic, goal-directed agents. Recent agent-interoperability protocols clarify two of the three edges of an agentic ecosystem (Anthropic's Model Context Protocol (MCP) standardizes the agent-to-tool edge, and Google's Agent2Agent (A2A) the agent-to-agent edge), but neither models the agent-to-instrument edge, where operations are stateful, safety-critical, exclusively owned, physically embodied, and produce measurements with units, calibration, and uncertainty. We present the Lab Agent Protocol (LAP), a protocol design that fills this gap. LAP retains A2A's peer-to-peer, discovery-first, task-lifecycle structure and adds four physical-world primitives: (i) the InstrumentCard, a signed capability and physical-limit description; (ii) first-class reservation for exclusive instrument and sample locking; (iii) a safety-fence handshake with operator-confirmation tokens cryptographically bound to a specific task and its parameters, gating hazardous and irreversible operations; and (iv) a MeasurementResult schema that makes every result physically typed (QUDT/UCUM), calibration-anchored, uncertainty-bearing, and reproducible by construction. We specify roles, a six-layer architecture, the JSON-RPC method set, the task and safety state machines, the error model, and cross-laboratory federation, and walk a closed-loop autonomous campaign through the protocol end-to-end. LAP is transport-compatible with the A2A/MCP ecosystem and encapsulates rather than replaces existing device standards such as SiLA 2 and OPC-UA.

The Model Context Protocol (MCP) has emerged as a transformative standard for connecting large language models (LLMs) with external data sources and tools, and has been rapidly adopted across personal applications and development platforms. However, existing benchmarks predominantly focus on generic information-seeking tools and fail to capture the practical challenges posed by personal social applications, where tools interact with individual accounts or local databases. To bridge this critical gap, we introduce MCP-Persona, the first benchmark specifically designed for evaluating agent performance on real-world, personalized MCP tools. MCP-Persona encompasses a diverse set of widely-used applications, ranging from social media platforms like Reddit and Xiaohongshu (Rednote) to enterprise collaboration suites such as Lark (Feishu) and Slack. Our extensive experiments on various state-of-the-art (SOTA) agents demonstrate their significant struggles with personalized tool use, thereby highlighting the benchmark's crucial role in identifying and addressing these limitations. MCP-Persona is publicly available at https://github.com/wwh0411/MCP-Persona}{https://github.com/wwh0411/MCP-Persona.

As Large Language Model (LLM) agents increasingly leverage the Model Context Protocol (MCP) to operate in complex environments, the expansion of their action spaces offers agents unsafe capabilities and underscores the risk of power-seeking. While broad action space and greater environment influence are essential for task fulfillment, they create a fragile risk surface where minor errors or hallucinations are magnified into catastrophic failures. In response, we propose SafeMCP, a {server-side} defense plugin that constrains tool acquisition via predictive reasoning regarding future safety risks. SafeMCP utilizes an internal world model for look-ahead reasoning to implement a two-tier defense: proactive tool filtering to constrain hazardous power expansion and immediate intervention as a fail-safe. To train SafeMCP, we introduce a three-stage pipeline comprising environmental dynamic grounding, safe policy initialization, and reinforcement learning (RL) with dual verifiable rewards. Experiments on PowerSeeking Bench, ToolEmu, and AgentHarm show that SafeMCP achieves a safe equilibrium, effectively mitigating risks while preserving agent utility.

Agent-memory frameworks -- mem0, Letta/MemGPT, Cognee, Zep/Graphiti, MemoryOS, MemTensor -- each ship their own SDK, storage layout, and operational vocabulary. There is no shared wire format: every integration is bespoke, every migration rebuilds memory from scratch, and no framework ships a governance surface that lets a human review writes before they enter long-term storage. We present memorywire, a JSON-Schema 2020-12 wire format for five memory operations (remember, recall, forget, merge, expire) over four memory types (semantic, episodic, procedural, emotional), with a MemoryStore interface, a fan-out router, and an optional HITL governance channel. We describe an open-source reference implementation with five backend adapters (sqlite-vec, mem0, Letta, Cognee, pgvector); a microbenchmark on a 100-fact / 50-query labelled corpus (42 with non-empty gold ids + 8 no-match probes) achieving recall@5 = 1.000 on the 42 gold-id queries with ingest p50 = 37.8 ms and recall p50 = 40.6 ms; an adversarial-fusion experiment showing Reciprocal Rank Fusion holds recall@5 = 1.000 across a 1-of-N rank-0 injection sweep (K in {0, 5, ..., 50}) where max fusion collapses to 0.500 with 80% leak at K >= 5; and a 16-scenario cross-adapter conformance suite passing 68 of 80 cells with zero failures. The contribution is not a new algorithm; it is a packaging of established components (RRF, FSMs, STM/LTM consolidation, diff-and-approve workflows) into a venue-neutral protocol with an empirically validated reference, positioned to compose with the Model Context Protocol rather than compete with it.

Regulated cybersecurity workflows lack a runtime substrate that enforces organization-level scope across retrieval, tool calls, memory, findings, reports, and audit while remaining model-agnostic and locally deployable. Recent large language model (LLM) agent systems report strong results on isolated cybersecurity tasks, yet they do not by themselves define an auditable platform architecture for regulated security operations centre (SOC) and compliance workflows, where a single analyst may trigger actions that bind the organization, and where the runtime must integrate with existing SIEM/XDR stacks as a primary source of context and alert-driven triggers rather than operate as a standalone analytical layer. This paper proposes an organization-scoped LLM agent runtime architecture for financial cybersecurity. The contribution is a typed Security Context that is created at every entry point, including SIEM/XDR notifications ingested as first-class triggers, and enforced at every component boundary, combined with a shared Runtime Core, logical specialist subagents, a governed Tool Adapter Layer exposing SIEM/XDR query, enrichment, and response primitives under uniform policy and audit, structured findings with evidence references, tiered human-in-the-loop (HITL) gates, and append-only audit. Model Context Protocol (MCP), extended telemetry, digital twins for pentesting, graph retrieval, and federated knowledge sharing are treated as optional extension paths rather than mandatory runtime assumptions. We describe an implementable slice as the architecture's testability surface, and we propose a falsifiable evaluation plan with metric-level pass criteria for architecture readiness, security-policy enforcement, evidence traceability, output quality, and operational observability.

MCP Server Proto-OKN (mcp-proto-okn) is a Python-based Model Context Protocol server that enables AI assistants to discover, inspect, query and integrate scientific knowledge graphs through natural language. The server provides graph routing, schema inspection, SPARQL execution, ontology expansion, multi-graph querying, and transcript generation, lowering the barrier to cross-domain knowledge graph analysis for biomedical and scientific users. mcp-proto-okn is implemented in Python using the FastMCP framework and is available at https://github.com/sbl-sdsc/mcp-proto-okn. Documentation, client configuration instructions, and example analysis transcripts are provided in the GitHub repository.

The era of the Internet of Agents (IoA) is taking shape: LLM agents are expected to fulfill user goals by orchestrating fast-growing populations of Model Context Protocol (MCP) servers, Agent-to-Agent (A2A) endpoints, reusable skills, and other LLM-callable services. Yet LLMs face a structural mismatch with this regime: effective context is a scarce resource that does not scale with the number of services. Concatenating thousands of service descriptions into a prompt overflows the context window, and even when the window is large enough, models systematically under-attend to information in the middle of long inputs, the well-documented Lost-in-the-Middle phenomenon. This is fundamentally a question of context management for service discovery. To address this, we propose an LLM-native progressive-disclosure scheme and its concrete instantiation, A2X (Agent-to-Anything service discovery): an LLM-driven pipeline that automatically organizes the registered services into a hierarchical taxonomy and walks it layer by layer at query time, so that every LLM call sees only a small candidate set highly relevant to the user query. This decouples effective-context scarcity from registry size and significantly reduces token consumption while improving retrieval accuracy. Compared to full-context dumping, A2X achieves a 6.2-point Hit Rate gain at one-ninth the prompt-token cost; compared to the state-of-the-art open-source embedding-based baseline, A2X improves Hit Rate by more than 20 points.

The rapid development of LLMs coupled with the introduction of Model Context Protocol (MCP) has revolutionized how intelligent agents interact with APIs through deterministic and structured methods \cite{ModelContextProtocolIntro2025}. While some existing systems like AutoMCP attempt to automate a previously completely manual process of generating MCP servers, they fail to address the recurring challenge of maintaining synchronization between evolving enterprise-level APIs and their corresponding MCP toolset implementation \cite{mastouri2025makingrestapisagentready}. This paper introduces DeltaMCP, a specification-aware, incremental regeneration tool for enterprise-grade MCP servers. DeltaMCP enables developers to only update the affected tooling of MCP servers, given a new release of it's corresponding service's OpenAPI specification. Using Azure REST API specifications as the evaluation dataset, DeltaMCP is benchmarked against baseline full generation methods on generation quality and system performance. The results demonstrate the reduction in developer overhead through DeltaMCP whilst improving maintainability and version consistency. This research offers a scalable approach for enterprises seeking to maintain high-fidelity, up-to-date MCP server infrastructures for LLM-based systems.

The integration of Large Language Models (LLMs) with microscopic traffic simulation offers a promising path toward autonomous urban planning and intelligent transportation analysis. However, existing monolithic agent architectures often struggle with the complexity of end-to-end simulation workflows, leading to reasoning failures, parameter inconsistency, and a lack of systematic state management. This paper proposes a novel multi-agent collaborative framework designed to automate the entire lifecycle of traffic simulation in SUMO (Simulation of Urban Mobility). Our approach decouples the simulation pipeline into specialized roles, including Planner, Builder, Demand, Runner, and Analyst, coordinated by a high-level reasoning engine. We introduce a state-persistent Orchestrator leveraging the Model Context Protocol (MCP) to ensure seamless data handover and environmental consistency across distributed agent actions. This architecture enables a robust closed-loop refinement process, where simulation outcomes are iteratively analyzed and optimized to satisfy user-defined Key Performance Indicators (KPIs). Experimental results through role ablation studies demonstrate that the proposed multi-agent framework significantly enhances task success rates and parameter accuracy compared to single-agent baselines. Furthermore, case studies on real-world network extraction and traffic optimization highlight the system's capability to bridge the gap between high-level natural language intent and low-level simulation execution.

The Model Context Protocol (MCP) standardizes how a large-language-model (LLM) agent and an external tool server exchange messages, but not trust: a host reads a server's self-declared tool list and dispatches calls, with no notion of which servers it may use, at what sensitivity, or which of a server's tools are in bounds. This work grew out of a concrete need -- letting the Enclawed agent use Google's externally-operated MCP servers (Gmail, Calendar, Drive) safely, admitting the server and bounding the tools it may drive, without changing MCP or Enclawed's own tool application-programming interface (API). The mechanism we built, mcp-attested (shipped in both the open enclawed-oss distribution and the enclaved flavor), generalizes: the gap that makes an unmediated third-party connection unsafe for one user makes a regulated deployment impossible to accredit. We close it with three additive mechanisms: (1) a small, offline-signed clearance assertion a server publishes at a well-known Uniform Resource Identifier (URI) and a host verifies against a pinned trust root before any tool dispatch; (2) a deny-by-default per-server tool allowlist, so admitting a server is not trusting its every tool; and (3) a flavor-gated enforcement mode that turns the checks from warnings into hard denials, with every decision written to a tamper-evident audit log. We give the wire format, the verification algorithm, a security analysis, and an LLM-driven adversarial evaluation; we then state the design in normative Request-for-Comments (RFC 2119) form -- schema, verification rules, error registry, well-known registration, and machine-checkable conformance vectors -- so it can be adopted as an MCP addendum rather than reinvented. An unextended host ignores the well-known document and behaves exactly as today.

The rise of tool-using Large Language Model (LLM) agents, standardized by protocols like the Model Context Protocol (MCP), has unlocked unprecedented autonomous execution capabilities for LLM Agents by integrating external open-domain knowledge and tools. However, this interoperability introduces a covert attack surface targeting the agent's cognitive planning layer. This paper systematically investigates Tool Description Poisoning (TDP), a novel semantic attack. In TDP, malicious instructions are not embedded in a tool's executable code, but rather covertly injected into its descriptive metadata, the very "manual" an agent relies on for secure planning and decision-making. To rigorously and systematically evaluate this emerging threat, we introduce the MCP-TDP Security Benchmark. This high-fidelity sandbox environment comprises 32 realistic, real-world test cases spanning 6 distinct risk categories. Our evaluation of 8 mainstream LLMs reveals severe vulnerabilities, with leading models like GPT-4o exhibiting a nearly 100% Attack Success Rate (ASR) in six high-risk scenarios. Furthermore, our findings demonstrate that common prompt-guardrail defenses are largely ineffective and can, counterintuitively, even be counterproductive (a phenomenon which we term the "Firewall Fallacy"). Crucially, we also propose a defense mechanism: "Reactive Self-Correction," where an agent autonomously detects and reverts its own malicious actions post-execution. This work provides the first specialized security benchmark tailored for TDP, offering essential insights for securing the cognitive and planning layers of advanced agentic systems.

Every Python function deployed as an LLM tool must today exist in two forms: an HTTP endpoint for human-facing clients and CI pipelines, and an MCP tool registration for agent runtimes such as Claude and Cursor. These representations share business logic yet diverge in all the surrounding machinery (routing, validation, serialisation, streaming, and schema maintenance), and they drift apart as the underlying code evolves. We present HarnessAPI, a Python framework that eliminates this duplication by treating a typed skill folder as the single source of truth. From one handler.py plus Pydantic schemas, the framework automatically derives a streaming HTTP endpoint with Server-Sent Events, an interactive OpenAPI/Swagger UI, and a zero-configuration MCP tool, all served from a single process. Dual-mode content negotiation lets the same handler serve SSE-streaming and JSON-returning clients with no handler changes. A dynamic code-generation mechanism ensures Pydantic type annotations propagate correctly to FastMCP's inspection layer, resolving a technical limitation that prevents naive closure-based registration. Measured across six representative skills using cloc, HarnessAPI reduces framework-facing boilerplate by 74% compared with a manually maintained dual-stack implementation (FastAPI server + FastMCP server). HarnessAPI subclasses FastAPI, inheriting its full middleware, dependency-injection, and deployment ecosystem. It is available at https://github.com/edwinjosechittilappilly/harnessapi and on PyPI (pip install harnessapi)