Agent Context Windows Stay Smart with Progressive Discovery MCP Server

By Zihao Lin
·8 min read

Cover Image for Agent Context Windows Stay Smart with Progressive Discovery MCP Server

The exciting thing about current AI isn't that it can talk, but that it can do things. As we transition from basic chatbots to self-operating systems capable of performing complex tasks, we encounter a problem known as the "context window."

Even though models like Gemini and Claude have context boxes that can hold millions of tokens, the "needle in a haystack" problem still exists. When you give an agent too much information, or too many tool meanings in the case of tool use, it becomes harder for them to think clearly.

This is where the Model Context Protocol (MCP) and the concept of "Progressive Discovery" become particularly important. Rather than cramming every possible tool definition into an agent at the beginning of a session, Progressive Discovery allows the agent to learn about its surroundings in a smart way, acquiring tools and context only when needed.

It's like the difference between knowing how to use an index and memorizing a full encyclopedia.

The Mechanics of Progressive Discovery in MCP

The Model Context Protocol facilitates consistent interaction between AI models and external data and tools. Traditionally, a developer could register a wide range of functions in the system prompt, from check_balance to update_database, sometimes as many as fifty.

This requires a substantial number of tokens, and surprisingly, it makes the model even more confused. If both search_users_v1 and search_users_v2 are present in the context simultaneously, the model may struggle to distinguish between them.

Progressive Discovery changes this way of thinking by using a file-system-like structure for tools. Initially, the worker has only one light tool, a "navigator" or "directory searcher". When the agent gets a request, it uses this navigator to find the right set of tools.

It then loads the descriptions of these tools in context and goes ahead to complete the request.

Why Architecture Matters in AI Agents Development

This method works in a manner similar to how humans think. We aren't always consciously aware of every skill we have. If developers use this "lazy loading" of brain resources as a model, they can make their programs run much better.

  • Token Efficiency Reduces Latency: When you only load the appropriate tool models (for example, only the five SQL tools and not the twenty Slack tools), you greatly lower the number of input tokens, which speeds up the Time-to-First-Token (TTFT) and lowers inference costs.

  • Hierarchical Tool Organization: You can set up your MCP server to group tools by function (for example, finance/, hr/, dev/, etc.), allowing the agent to follow a sensible path instead of having to guess from a list.

  • Better Accuracy: With fewer things that could be confused with similar patterns, the model's attention mechanism can focus entirely on the relevant models, which means that hallucinated function calls are much less common.

Building Trust: The Sociology of Smart Context

Moving to Progressive Discovery is not just a technical improvement; it is necessary for using bots in high-stakes settings such as healthcare or financial services. Sociologically, faith in technology is weak. It depends on "predictable competence." When an agent has too much information, it gets "distracted" and makes mistakes that make users lose trust.

In fields like data analytics, where accuracy is crucial, an agent is worthless if it identifies a data trend that isn't there due to mixing up two similar API addresses. However, if the context is set up in real time, the agent will act more like a specialized expert and less like a generalist who is guessing the answers.

Research Insight: Trust and Complexity

New studies reveal that the relationship between system complexity and user trust is not straightforward. A 2024 study in the National Library of Medicine examines how people learn to accept AI beings. The results show that confidence isn't something that can be turned on or off, but rather a back-and-forth conversation that depends on how the other person is perceived as being able to do difficult things correctly.

In one example, in the case of digital loans, borrowers adjust their behavior based on whether they perceive the digital middleman as "competent" or merely "automated." You can read the study here to learn about people's perceptions of AI agents and their level of trust in them.

  • Cognitive Load Management: People trust decision-making helpers that make things easier, not ones that make things more difficult. Progressive Discovery aligns the agent's "thinking" with people's understanding of logical retrieval.

  • Risk Mitigation in Fintech: When an agent uses Progressive Discovery in digital lending, they are less likely to accidentally activate a "deny loan" function intended for a different process, as that tool wouldn't be available when the agent checks the progress of a request.

  • Transparency Promotes Adoption: When an agent clearly "searches" for the right tools, it leaves a record of its thought process that others can see, which is important for compliance in industries with strict rules.

Optimizing the Agentic Workflow

Using Progressive Discovery requires us to change how we make AI agents. It shifts the difficulty from the early work on prompts to the server-side design. The MCP server becomes a smart link, rather than a dumb pipe.

For the creator, this means that the main goal becomes setting clear, meaningful limits on what each tool can do. You aren't just writing Python functions anymore; you're building a list of what your program can do. This structural work ensures that when an agent selects a tool, it receives exactly what it intended to receive.

Additionally, this design enables the use of more advanced data analysis tools. The person responsible for reviewing the quarterly income doesn't need to be familiar with the code-deployment tools.

If you keep these sites completely separate through Progressive Discovery, the analytics agent will stay analytical.

The Educational Foundation

There is more to building these complex systems than just knowing how to code; you also need to understand a great deal about how data is organized and accessed. Klavis and similar tools do most of the protocol work, but the architectural reasoning is often based on complex academic ideas.

It is common for individuals who have earned a data analytics master degree to be proficient in dealing with these taxonomies, as the course often includes advanced topics such as database design and information retrieval systems. These are directly useful for organizing MCP servers.

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Source: Pexels

Implementing Progressive Discovery: A Strategic Guide

Start small to make this work in your system. You don't have to completely overhaul your whole agent environment right away. Begin with your most "tool-heavy" agent, likely the one that frequently reaches the context limit.

  • Take a look at your Tool Registry: Review your tool list and identify the groups. It's normal to want to separate things that are mixed together. Having 10 tools for Jira and 10 for GitHub indicates a need to separate these two groups.

  • Create a "Router" Tool: Develop a simple router that provides the correct tool definitions for any name you input. This is an early form of Progressive Discovery.

  • Keep an eye on the "Discovery" Step: Pay attention to how your agent searches. If it always looks for "everything," that means your topic might need to be revised so that it can consider things in more detail.

This approach significantly reduces the development time for AI bots. Debugging is easier when you know exactly what "directory" of tools the agent loaded before it failed. It isolates variables, which makes AI's black box of thinking a little easier to see.

Additionally, if you are on a team that performs extensive data mining, this feature allows you to set very specific permissions. You can set up the MCP server so that it only shows "User Data" tools after the agent has passed a "Security Check." This adds an extra layer of security to the process of finding information.

Key Insights

  • Context: Hygiene is Important: Just because an LLM can handle 100 tools doesn't mean it is right to do so. Progressive Discovery makes the context window clear and on point.

  • Latency vs. Capability: By dynamically loading tools, you can reduce the size of the initial payload, which saves money and accelerates exchanges while still providing the agent with a wide range of capabilities.

  • Trust Through Structure: Sociological studies on human-AI trust, particularly in sensitive areas such as finance, demonstrate that organizing tools in a rational manner reduces the risk of misperceptions.

  • Data-Driven Design: The way your MCP server is configured should illustrate how your data flows from one point to another. This is a skill that is often learned and practiced in more advanced analytics courses.

FAQs

  • Does Progressive Discovery increase the number of model round-trips?
  • It can add one first step (the "finding" step), but it usually saves time in the end. By making the context smaller, the next steps get faster, and the better accuracy means that the agent doesn't have to go through "correction loops," which are situations where it fails and retries.
  • Is this only for Python-based agents?
  • No. The Model Context Protocol is compatible with any programming language. Progressive Discovery is an architectural scheme that can be used with any language that works with MCP. Even though it can be used with other languages, Python and TypeScript are the most popular choices.
  • How does this impact data analytics tasks specifically?
  • It enables robots to work with large datasets more efficiently. The agent can keep its logic sharp and its math exact by loading only the "statistical regression" tools when needed, rather than loading every possible analysis function.