graph-evolution

Graph Evolution

Builds Trailmark code graphs at two source snapshots and computes a

structural diff. Surfaces security-relevant changes that text-level

diffs miss: new attack paths, complexity shifts, blast radius growth,

taint propagation changes, and privilege boundary modifications.

When to Use

• Comparing two git refs to understand what structurally changed
• Auditing a range of commits for security-relevant evolution
• Detecting new attack paths created by code changes
• Finding functions whose blast radius or complexity grew silently
• Identifying taint propagation changes across refactors
• Pre-release structural comparison (tag-to-tag or branch-to-branch)

When NOT to Use

• Line-level code review (use differential-review for text-diff analysis)
• Single-snapshot analysis (use the trailmark skill directly)
• Diagram generation from a single snapshot (use the diagramming-code skill)
• Mutation testing triage (use the genotoxic skill)

Rationalizations to Reject

| Rationalization | Why It's Wrong | Required Action |

|-----------------|----------------|-----------------|

| "We just need the structural diff, skip pre-analysis" | Without pre-analysis, you miss taint changes, blast radius growth, and privilege boundary shifts | Run engine.preanalysis() on both snapshots |

| "Text diff covers what changed" | Text diffs miss new attack paths, transitive complexity shifts, and subgraph membership changes | Use structural diff to complement text diff |

| "Only added nodes matter" | Removed security functions and shifted privilege boundaries are equally dangerous | Review removals and modifications, not just additions |

| "Low-severity structural changes can be ignored" | INFO-level changes (dead code removal) can mask removed security checks | Classify every change, review removals for replaced functionality |

| "One snapshot's graph is enough for comparison" | Single-snapshot analysis can't detect evolution — you need both before and after | Always build and export both graphs |

| "Tool isn't installed, I'll compare manually" | Manual comparison misses what graph analysis catches | Install trailmark first |

| "The diff came back empty, so nothing changed structurally" | trailmark diff defaults --language to python and exits 0 with empty arrays on any other target, so an empty diff reads identically whether the code is unchanged or the language was wrong | Pass --language explicitly and re-run before concluding no change |

---

Prerequisites

trailmark must be installed. If uv run trailmark fails, run:

uv tool install trailmark
# Python snippets: uv run --with trailmark python -   (a tool env is not importable)

DO NOT fall back to "manual comparison" or reading source files as a

substitute for running trailmark. The tool must be installed and used

programmatically. If installation fails, report the error.

---

Quick Start

# Compare two git refs (e.g., tags, branches, commits)
# 1. Build graphs at each snapshot
# 2. Run pre-analysis on both
# 3. Compute structural diff
# 4. Generate report

# Step-by-step: see Workflow below

---

Decision Tree

├─ Need to understand what each metric means?
│  └─ Read: references/evolution-metrics.md
│
├─ Need the report output format?
│  └─ Read: references/report-format.md
│
├─ Already have two graph JSON exports?
│  └─ Jump to Phase 3 (run native diff + graph_diff.py)
│
└─ Starting from two git refs?
   └─ Start at Phase 1

---

Workflow

Graph Evolution Progress:
- [ ] Phase 1: Create snapshots (git worktrees)
- [ ] Phase 2: Build graphs + pre-analysis on both snapshots
- [ ] Phase 3: Compute structural diff
- [ ] Phase 4: Interpret diff and generate report
- [ ] Phase 5: Clean up worktrees

Phase 1: Create Snapshots

Use git worktrees to get clean copies of each ref without disturbing

the working tree.

# Create temp directories for worktrees
BEFORE_DIR=$(mktemp -d)
AFTER_DIR=$(mktemp -d)

# Create worktrees (run from repo root)
git worktree add "$BEFORE_DIR" {before_ref}
git worktree add "$AFTER_DIR" {after_ref}

If comparing two directories instead of git refs, skip this phase and

use the directory paths directly in Phase 2.

Phase 2: Build Graphs and Run Pre-Analysis

Build Trailmark graphs for both snapshots and run pre-analysis on each.

Pre-analysis computes blast radius, taint propagation, privilege

boundaries, and entrypoint enumeration.

from trailmark.query.api import QueryEngine

def build_and_export(target_dir, output_path, language="auto"):
    """Build graph, run pre-analysis, export JSON."""
    engine = QueryEngine.from_directory(target_dir, language=language)
    engine.preanalysis()
    json_str = engine.to_json()
    with open(output_path, "w") as f:
        f.write(json_str)
    return engine.summary()

import tempfile, os
work_dir = tempfile.mkdtemp(prefix="trailmark_evolution_")
before_json = os.path.join(work_dir, "before_graph.json")
after_json = os.path.join(work_dir, "after_graph.json")

before_summary = build_and_export(
    "{before_dir}", before_json
)
after_summary = build_and_export(
    "{after_dir}", after_json
)

Verify both graphs built successfully by checking the summary output.

If either fails, rerun with an explicit language or comma-separated list

instead of auto.

Phase 3: Compute Structural Diff

Run both:

1. Trailmark's native structural diff for nodes, edges, and entrypoints
2. The plugin's graph_diff.py helper for subgraph membership changes

Use the same work_dir from Phase 2, and pass the same --language value Phase 2

built with. trailmark diff defaults that flag to python, so on any other

target the default exits 0 and writes empty arrays rather than reporting a

mismatch.

trailmark diff --json --language auto "{before_dir}" "{after_dir}" > "{work_dir}/trailmark_diff.json" || \
  uv run trailmark diff --json --language auto "{before_dir}" "{after_dir}" > "{work_dir}/trailmark_diff.json"

uv run {baseDir}/scripts/graph_diff.py \
    --before "{before_json}" \
    --after "{after_json}" > "{work_dir}/subgraph_diff.json"

If Phase 2 needed an explicit language or a comma-separated list instead of

auto, use that same value here.

If either diff command fails or writes an empty JSON file, stop and report the

error instead of continuing to Phase 4.

A trailmark_diff.json whose nodes, edges, and entrypoints arrays are all

empty means either nothing changed structurally or both snapshots parsed to

(near-)empty graphs. Decide which using Phase 2's graph summaries: if either

snapshot's node count is zero or implausibly small for the target, the parse

missed the code — name the language set explicitly (rust, solidity,

python,rust) and re-run. Healthy node counts on both snapshots plus an empty

diff is genuine structural stability.

The native Trailmark diff contains:

| Key | Contents |

|-----|----------|

| summary_delta | Changes in node/edge/entrypoint counts |

| nodes.added | New functions, classes, methods |

| nodes.removed | Deleted functions, classes, methods |

| nodes.modified | Functions with changed CC, params, line span |

| edges.added | New call/inheritance/import relationships |

| edges.removed | Deleted relationships |

| entrypoints | Added, removed, and modified entrypoints |

The subgraph diff contains:

| Key | Contents |

|-----|----------|

| subgraphs | Per-subgraph membership changes (tainted, high_blast_radius, etc.) |

Phase 4: Interpret Diff and Generate Report

Read both diff JSON files and generate a security-focused markdown

report.

See [references/report-format.md](references/report-format.md) for

the full template.

Interpretation priorities (highest to lowest):

1. New tainted paths — nodes entering the tainted subgraph,

especially if they also appear in added edges targeting sensitive

functions

1. Privilege boundary changes — new or removed trust transitions

from the native entrypoint/edge diff plus the subgraph diff

1. Attack surface growth — new entrypoints, especially

untrusted_external, from trailmark_diff.json

1. Blast radius increases — nodes entering high_blast_radius
2. Complexity spikes — CC increases > 3 on tainted or

entrypoint-reachable nodes

1. Structural additions — new nodes and edges (review needed)
2. Structural removals — verify removed security functions were

replaced

Cross-reference structural changes with git diff {before_ref}..{after_ref}

to add source-level context to findings.

Severity classification:

| Severity | Structural Signal |

|----------|------------------|

| CRITICAL | New tainted path to sensitive function, removed auth boundary |

| HIGH | New entrypoint + high blast radius, large CC increase on tainted node |

| MEDIUM | New trust-boundary-crossing edges, moderate CC increase |

| LOW | Added nodes without entrypoint reachability |

| INFO | Dead code removal, complexity reductions |

For detailed metric definitions, see

[references/evolution-metrics.md](references/evolution-metrics.md).

Phase 5: Clean Up

Remove git worktrees after the report is written:

git worktree remove "{before_dir}"
git worktree remove "{after_dir}"

---

Diff Reference

trailmark diff --json --language auto BEFORE AFTER
uv run {baseDir}/scripts/graph_diff.py [OPTIONS]

trailmark diff --language defaults to python. On a target in any other

language that default still exits 0, emitting well-formed JSON with empty

nodes, edges, and entrypoints arrays, so always pass the flag: auto

detects and merges every supported language found under the target, and a single

name (rust, solidity) or comma-separated list (python,rust) pins an

explicit set. auto fails loudly with `No supported languages detected under

<path>` when a snapshot holds nothing it can parse, which is the outcome you

want. Confirm the language first; only then can an empty diff count as evidence

that nothing changed.

Use trailmark diff for:

• Node/edge changes
• Added/removed/modified entrypoints
• Human-readable structural diff reports

Use graph_diff.py for:

• Subgraph membership changes derived from engine.preanalysis()
• tainted, high_blast_radius, privilege_boundary, and related sets

| Argument | Default | Description |

|----------|---------|-------------|

| --before | required | Path to the "before" graph JSON |

| --after | required | Path to the "after" graph JSON |

| --indent | 2 | JSON output indentation |

graph_diff.py input format: Trailmark JSON exports from engine.to_json().

graph_diff.py output: JSON structural diff for nodes, edges, and subgraphs.

---

Quality Checklist

Before delivering the report:

• [ ] Both graphs built successfully (check summaries)
• [ ] Pre-analysis ran on both snapshots
• [ ] Native Trailmark diff computed (trailmark_diff.json); if it is empty,

both snapshots' Phase 2 node counts were non-zero, so empty means stable

• [ ] Subgraph diff computed and non-empty (subgraph_diff.json)
• [ ] All subgraph changes interpreted (tainted, blast radius, etc.)
• [ ] Critical findings include evidence (node IDs, edge diffs)
• [ ] Severity levels assigned to all findings
• [ ] Source-level context added via git diff cross-reference
• [ ] Worktrees cleaned up (or temp dirs removed)
• [ ] Report written to GRAPH_EVOLUTION_*.md

---

Integration

trailmark skill:

Phase 2 uses the trailmark API for graph building and pre-analysis.

All trailmark query patterns work on either snapshot's engine.

differential-review skill:

Use graph-evolution for structural analysis, differential-review for

line-level code review. The two are complementary — graph-evolution

finds attack paths that text diffs miss, while differential-review

provides git blame context and micro-adversarial analysis.

trailmark-review-gate skill:

Use trailmark-review-gate after graph-evolution when a branch, pull request,

fix commit, or release diff needs a PASS/WARN/FAIL/UNKNOWN structural review

packet. The gate applies deterministic review rules to graph-evolution output;

it does not replace human review.

genotoxic skill:

If graph-evolution reveals new high-CC tainted nodes, feed them to

genotoxic for mutation testing triage.

diagramming-code skill:

Generate before/after diagrams to visualize structural changes.

Use call-graph or data-flow diagrams focused on changed nodes.

---

Supporting Documentation

• [references/evolution-metrics.md](references/evolution-metrics.md) —

What each structural metric means and why it matters for security

• [references/report-format.md](references/report-format.md) —

Report template, severity classification, and example findings