Read your code graph and clean up your repos

A code graph with a few thousand nodes looks like a mess the first time you open it. This recipe shows you how to read it in order, from the big picture down to single functions. You’ll finish with a short list of dead and duplicate code that your coding agent can check before anything is deleted.

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The scenario

A small team, mostly not engineers, ran their product on 12 repositories that grew one feature at a time. They connected the repositories to Graphify and opened Graphs. The graph had about 3,400 nodes, and they didn’t know what to do with it. Every view in this recipe was already in their Console. They just hadn’t found it yet. In one session they learned which code areas held the product together, which functions they shouldn’t touch casually, and which code nobody was calling.

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What you’ll build

• A sense of which code areas your repositories contain and how they connect.
• A short list of the functions most of your code depends on.
• A check of what one change could reach, one to three steps out.
• A list of dead code and duplicate code, with the evidence for each finding.
• A cleanup task your agent investigates before it changes anything.

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Setup

You need a Graphify workspace with at least one indexed repository. If you haven’t got one yet, follow the quickstart. For a graph that spans several repositories, combine them first.

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Step 1: Start from the overview

Open Overview. Your indexed repositories lists what Graphify has built. Workspace stats and Graph density show how big and how connected your graph is. The Code findings tile counts what the repository checks found. Select View all to open the full list later, in Step 5.

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Step 2: Read the code areas

Open Graphs and pick a repository. Each colour on the canvas is a code area: a group of files and functions that connect more to each other than to the rest of the code. Open Graph guide to see what the colours, lines and highlights mean.

• Code areas lists the areas in full screen. Clear Select all, then tick one or two areas to see them on their own.
• Select a node, then select its code area in the node details to show only that area on the canvas.
• On very large graphs, the canvas starts in the Code area view, which groups nodes into areas until you search for one. A graph this size opens with every node visible.

In the scenario, the team found that most of the 3,400 nodes sat in a few large areas, and that most of the 12 repositories formed areas of their own.

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Step 3: Find what’s most connected

Most connected lists the nodes with the most connections, along with their count. These are the functions and modules that much of your code depends on. Colours match the code areas, so you can see which area each one belongs to. Select a row to open its node details. Connections shows how many links come in, how many go out, and how many cross into another repository. Select Explain this code to ask Graphify what it does, with citations.

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Step 4: Check what a change could affect

In the node details, find What a change could affect. If you see No dependents found in this view, read the note under it. Graphify only checked the nodes it has loaded, and dynamic and external callers may not be represented. For a deeper check, see Plan a refactor.

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Step 5: Find dead code and duplicate code

Select Code findings in the graph header, or View all on the Overview tile. Repository findings come in two kinds. These checks cover Python, JavaScript and TypeScript. Select a finding, then What was checked to see its evidence. Show in graph puts it on the canvas. If a finding is intentional, use Hide or give feedback. Include findings I hid brings them back. Read more in Insights.

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Step 6: Read the wiki for context

If your workspace has Wiki, open it to read about each code area in plain language. Articles lists the pages. Each page shows Key components and links you back with Show in graph or Open the source. Every statement is marked Verified, Inferred or Needs review, and pages say which model wrote them, so treat Inferred text as a lead to check. Use Ask the wiki for questions like “what does this area do?”. See Wiki.

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Step 7: Hand the findings to your agent

Open a finding and select Copy task for my agent. Use Preview or edit the task first if you want to add context. After you copy it, the Console confirms that no code was changed. The copied task tells your agent not to delete code, apply a change, open a pull request, or merge anything without your separate instruction. It asks the agent to return its investigation and a proposed next step first. Paste it into your agent, read what it finds, and only then approve the change. For your agent to check callers against the graph while it works, connect it to the hosted MCP server and follow Make your agent use the graph.

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When it goes wrong

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What you built

You read your graph from the top down: its code areas, its most connected code, and what one change reaches. You turned the dead and duplicate code findings into a task your agent investigates before it changes anything. To see how sure Graphify is of each connection, read Provenance.

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Next steps