diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e6e0f7da8cd3..b872e9fe3cd0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -32,8 +32,8 @@ jobs:
             code:
               - '!documentation/**'
 
-  rust-format:
-    name: Check Rust Code Format
+  structure-check:
+    name: Repository Structure Checks
     runs-on: ubuntu-latest
     needs: changes
     if: needs.changes.outputs.code == 'true' || github.event_name != 'pull_request'
@@ -41,10 +41,13 @@ jobs:
       - name: Checkout Code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # pin@v4
 
-      - uses: actions-rust-lang/setup-rust-toolchain@v1
+      - name: Set up Rust toolchain
+        uses: actions-rust-lang/setup-rust-toolchain@v1
 
-      - name: Run cargo fmt
-        run: cargo fmt --check
+      - name: Run structure checks
+        run: |
+          source ./bin/activate-hermit
+          just structure-check
 
   rust-build-and-test:
     name: Build and Test Rust Project
diff --git a/Justfile b/Justfile
index ce16e0a622b4..3009c0f8b848 100644
--- a/Justfile
+++ b/Justfile
@@ -4,19 +4,50 @@
 default:
   @just --list
 
+# Run repository structure checks
+structure-check:
+    #!/usr/bin/env bash
+    set -e
+    echo "Running repository structure checks..."
+
+    # Find all executable scripts
+    # Use -perm for BSD/macOS compatibility (GNU find uses -executable)
+    mapfile -t scripts < <(find scripts/ci/structure -name "*.sh" -type f \( -perm -u=x -o -perm -g=x -o -perm -o=x \) 2>/dev/null | sort)
+
+    if [ ${#scripts[@]} -eq 0 ]; then
+        echo "ERROR: No structure check scripts found in scripts/ci/structure/"
+        exit 1
+    fi
+
+    for script in "${scripts[@]}"; do
+        echo ""
+        echo "========================================"
+        echo "Running: $script"
+        echo "========================================"
+        "$script" || exit 1
+    done
+
+    echo ""
+    echo "All structure checks passed"
+
 # Run all style checks and formatting (precommit validation)
 check-everything:
-    @echo "🔧 RUNNING ALL STYLE CHECKS..."
-    @echo "  → Formatting Rust code..."
-    cargo fmt --all
-    @echo "  → Running clippy linting..."
+    #!/usr/bin/env bash
+    set -e
+    echo "RUNNING ALL STYLE CHECKS..."
+    echo ""
+    just structure-check
+    echo ""
+    echo "Running clippy linting..."
     ./scripts/clippy-lint.sh
-    @echo "  → Checking UI code formatting..."
+    echo ""
+    echo "Checking UI code formatting..."
     cd ui/desktop && npm run lint:check
-    @echo "  → Validating OpenAPI schema..."
+    echo ""
+    echo "Validating OpenAPI schema..."
     ./scripts/check-openapi-schema.sh
-    @echo ""
-    @echo "✅ All style checks passed!"
+    echo ""
+    echo "All style checks passed!"
 
 # Default release command
 release-binary:
diff --git a/scripts/ci/structure/README.md b/scripts/ci/structure/README.md
new file mode 100644
index 000000000000..05fa12f7a925
--- /dev/null
+++ b/scripts/ci/structure/README.md
@@ -0,0 +1,63 @@
+# Repository Structure Checks
+
+This directory contains scripts that perform static analysis and structural validation of the repository **before** any builds are executed. These checks enforce repository policies and prevent issues from being committed.
+
+## How It Works
+
+All executable shell scripts (`*.sh`) in this directory are automatically run by:
+- **CI**: `.github/workflows/ci.yml` - `structure-check` job
+- **Local**: `just check-everything` command
+
+Scripts are executed in alphabetical order. All scripts must pass for the check to succeed.
+
+## Adding a New Check
+
+1. Create a new executable shell script in this directory:
+   ```bash
+   touch scripts/ci/structure/check-your-thing.sh
+   chmod +x scripts/ci/structure/check-your-thing.sh
+   ```
+
+2. Write your check script following this template:
+   ```bash
+   #!/usr/bin/env bash
+   set -e
+
+   # Brief description of what this checks
+
+   echo "Checking your thing..."
+
+   # Your validation logic here
+   if ! validation_passes; then
+     echo ""
+     echo "ERROR: Your thing validation failed"
+     echo ""
+     echo "To fix this issue:"
+     echo "  some-command-to-fix-it"
+     echo ""
+     exit 1
+   fi
+
+   echo "Your thing is valid"
+   ```
+
+3. Test locally:
+   ```bash
+   ./scripts/ci/structure/check-your-thing.sh
+   just check-everything
+   ```
+
+4. Commit and push - CI will automatically run your new check
+
+## Existing Checks
+
+- **check-prebuilt-binaries.sh** - Prevents prebuilt executables from being committed (security)
+- **check-rust-format.sh** - Validates Rust code formatting
+
+## Guidelines
+
+- **Keep checks fast** - These run on every PR
+- **Make errors actionable** - Tell users how to fix issues
+- **Exit codes** - Exit 0 for success, non-zero for failure
+- **Echo progress** - Let users know what's being checked
+- **Use allowlists sparingly** - Only for temporary exceptions
diff --git a/scripts/ci/structure/check-prebuilt-binaries.sh b/scripts/ci/structure/check-prebuilt-binaries.sh
new file mode 100755
index 000000000000..ca24201219e1
--- /dev/null
+++ b/scripts/ci/structure/check-prebuilt-binaries.sh
@@ -0,0 +1,172 @@
+#!/usr/bin/env bash
+set -e
+
+# Check for prebuilt executables/binaries in the repository
+# This is a security measure to prevent supply chain attacks via checked-in binaries
+#
+# Similar checks in other projects:
+# - Rust compiler: https://github.com/rust-lang/rust/blob/master/src/tools/tidy/src/bins.rs
+# - OSSF Scorecard: https://github.com/ossf/scorecard/blob/main/checks/binary_artifact.go
+
+echo "Checking for prebuilt executables and binaries..."
+
+# Allowlist for existing binaries (TEMPORARY - to be removed)
+# These binaries should be removed and built from source or downloaded at build time
+# Added in: https://github.com/block/goose/pull/880 (commit cfd3ee8fd9c)
+declare -A allowlist=(
+  ["ui/desktop/src/platform/windows/bin/libgcc_s_seh-1.dll"]=1
+  ["ui/desktop/src/platform/windows/bin/libstdc++-6.dll"]=1
+  ["ui/desktop/src/platform/windows/bin/libwinpthread-1.dll"]=1
+  ["ui/desktop/src/platform/windows/bin/uv.exe"]=1
+  ["ui/desktop/src/platform/windows/bin/uvx.exe"]=1
+)
+
+# Denylist of file type patterns that indicate binary executables or libraries
+# These patterns match against the output of the 'file' command
+denylist_patterns=(
+  "PE32.*executable"
+  "PE32.*DLL"
+  "MS-DOS executable"
+  "ELF.*executable"
+  "ELF.*shared object"
+  "Mach-O.*executable"
+  "Mach-O.*dynamically linked shared library"
+  "Mach-O.*bundle"
+  "Java archive data"
+  "compiled Java class"
+  "python.*byte-compiled"
+  "WebAssembly"
+  "current ar archive"
+)
+
+# Associative arrays for fast O(1) lookups
+declare -A violations
+declare -A allowlisted_files
+declare -A checked_files
+
+echo "Scanning git-tracked files..."
+
+# Collect all git-tracked files
+mapfile -t all_files < <(git ls-files)
+
+echo "Checking ${#all_files[@]} tracked files..."
+
+# First pass: Quick extension check (no file command needed)
+extension_regex='\.(exe|dll|so|dylib|a|o|bin|app|wasm|jar|class|pyc|pyd|pyo|lib)$'
+
+for file in "${all_files[@]}"; do
+  # Skip if not a regular file or if it's a symlink
+  [ -f "$file" ] && [ ! -L "$file" ] || continue
+
+  # Use bash regex matching (no grep subprocess)
+  if [[ "$file" =~ $extension_regex ]]; then
+    checked_files["$file"]=1
+
+    if [[ -n "${allowlist[$file]}" ]]; then
+      allowlisted_files["$file"]=1
+    else
+      violations["$file"]=1
+    fi
+  fi
+done
+
+echo "Found ${#violations[@]} files with suspicious extensions"
+
+# Second pass: Batch check remaining files with ONE file command
+# Build list of files not yet checked
+files_to_check=()
+for file in "${all_files[@]}"; do
+  # Skip if not a regular file or if it's a symlink
+  [ -f "$file" ] && [ ! -L "$file" ] || continue
+  [[ -z "${checked_files[$file]}" ]] || continue
+  files_to_check+=("$file")
+done
+
+if [ ${#files_to_check[@]} -gt 0 ]; then
+  echo "Deep scanning ${#files_to_check[@]} additional files..."
+
+  # Use xargs to batch process files (handles ARG_MAX limits, processes in chunks of 100)
+  # Use process substitution instead of pipe to avoid subshell
+  while IFS=: read -r filepath description; do
+    # Check if description matches any denylist pattern
+    is_binary=false
+    for pattern in "${denylist_patterns[@]}"; do
+      if [[ "$description" =~ $pattern ]]; then
+        is_binary=true
+        break
+      fi
+    done
+
+    if [ "$is_binary" = true ]; then
+      if [[ -n "${allowlist[$filepath]}" ]]; then
+        allowlisted_files["$filepath"]=1
+      else
+        violations["$filepath"]=1
+      fi
+    fi
+  done < <(printf '%s\n' "${files_to_check[@]}" | xargs -n 100 -P 1 file 2>/dev/null)
+fi
+
+# Report allowlisted files
+if [ ${#allowlisted_files[@]} -gt 0 ]; then
+  echo ""
+  echo "WARNING: The following binaries are temporarily allowlisted:"
+  echo ""
+
+  for file in "${!allowlisted_files[@]}"; do
+    echo "  [ALLOWLISTED] $file"
+    if [ -f "$file" ]; then
+      echo "                $(file -b "$file")"
+      echo "                Size: $(du -h "$file" | cut -f1)"
+    fi
+    echo ""
+  done
+
+  echo "These files should be removed and replaced with build-time solutions."
+  echo ""
+fi
+
+# Report violations
+if [ ${#violations[@]} -gt 0 ]; then
+  echo ""
+  echo "ERROR: PREBUILT BINARIES DETECTED!"
+  echo ""
+  echo "The following prebuilt executables or binary files were found in the repository:"
+  echo ""
+
+  for file in "${!violations[@]}"; do
+    echo "  [VIOLATION] $file"
+    echo "              $(file -b "$file")"
+    if [ -f "$file" ]; then
+      echo "              Size: $(du -h "$file" | cut -f1)"
+    fi
+    echo ""
+  done
+
+  echo "========================================================================"
+  echo ""
+  echo "POLICY: Prebuilt binaries are not allowed in this repository"
+  echo ""
+  echo "This is a security measure to prevent supply chain attacks."
+  echo "All executables must be built from source in CI/CD pipelines."
+  echo ""
+  echo "If you need platform-specific binaries:"
+  echo "  1. Build them in the GitHub Actions workflow"
+  echo "  2. Use package managers (npm, cargo, apt, brew, etc.)"
+  echo "  3. Download from trusted sources during build time"
+  echo "  4. Add checksums/signatures verification"
+  echo ""
+  echo "To remove these files:"
+  for file in "${!violations[@]}"; do
+    echo "  git rm \"$file\""
+  done
+  echo ""
+  echo "If this is a false positive, add the file to the allowlist in:"
+  echo "  scripts/ci/structure/check-prebuilt-binaries.sh"
+  echo ""
+  echo "========================================================================"
+
+  exit 1
+fi
+
+echo "No new prebuilt binaries detected (${#allowlisted_files[@]} allowlisted)"
diff --git a/scripts/ci/structure/check-rust-format.sh b/scripts/ci/structure/check-rust-format.sh
new file mode 100755
index 000000000000..46ee5b9e7fd1
--- /dev/null
+++ b/scripts/ci/structure/check-rust-format.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+set -e
+
+# Check Rust code formatting
+
+echo "Checking Rust code formatting..."
+
+if ! cargo fmt --all --check; then
+  echo ""
+  echo "ERROR: Rust code is not properly formatted"
+  echo ""
+  echo "To fix this issue:"
+  echo "  cargo fmt --all"
+  echo ""
+  exit 1
+fi
+
+echo "Rust code formatting is correct"