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      <h1>CLI Usage</h1>

      <h2 id="testing">Testing / QA</h2>
      <p class="muted">Run these commands to confirm Clinstruct-cli works end-to-end (recommended before submission).</p>
      <pre class="code-block"><code># Run full test suite
cargo test --all

# One-command smoke test
./scripts/smoke.sh

# Strict fixtures must exit 0
cargo run -- selftest --fixtures tests/fixtures/clean/soap --template soap --strict
cargo run -- selftest --fixtures tests/fixtures/clean/hp --template hp --strict
cargo run -- selftest --fixtures tests/fixtures/clean/discharge --template discharge --strict</code></pre>

      <p class="muted"><strong>Note:</strong> Product name is Clinstruct-cli; the CLI command/binary name is <code>clinote</code>.</p>
      <pre class="code-block"><code>clinote parse --input note.txt --format soap \
  --out out.json --out-format json --bundle auto

clinote batch --input-dir notes --glob "*.txt" \
  --format hp --out-dir outputs --out-format csv

clinote sample --out-dir samples --n 6 --bundles 2

clinote validate --config clinote.toml</code></pre>

      <h2>CLI Commands</h2>
      <pre class="code-block"><code># Validate a note (strict mode + exit code 2 on errors)
clinote validate notes.txt --template soap --strict

# Preview detected sections with line counts
clinote preview notes.txt --template hp

# Selftest a directory (recursive) and export outputs
clinote selftest --fixtures tests/fixtures --template soap --out selftest_outputs

# Selftest with glob + JSON summary
clinote selftest --fixtures "tests/fixtures/*.txt" --template discharge --json</code></pre>

      <ul class="doc-list">
        <li><strong>Validate strict:</strong> missing required sections are errors (exit code 2). Non-strict treats them as warnings (exit code 0).</li>
        <li><strong>Preview:</strong> prints detected sections plus line/character counts.</li>
        <li><strong>Selftest:</strong> scans a folder or glob, validates notes, and reports totals + top failures.</li>
      </ul>

      <h2>Config reference</h2>
      <pre class="code-block"><code>[formats.soap]
section_order = ["Subjective", "Objective", "Assessment", "Plan"]

heading_aliases = { "Hx" = "PMH", "Dx" = "Assessment" }

enable_fallback_heuristics = true

[bundle]
mode_default = "auto"
delimiters = ["----- NOTE -----", "=== VISIT ==="]

[csv]
layout = "wide"

glob_default = "*.txt"</code></pre>

      <h2>Bundle mode</h2>
      <ul class="doc-list">
        <li><strong>auto</strong>: split only when delimiters or timestamps appear multiple times.</li>
        <li><strong>on</strong>: attempt to split and warn if delimiters are not found.</li>
        <li><strong>off</strong>: treat input as a single note.</li>
      </ul>

      <h2>Interactive mode</h2>
      <p>Use <code>--interactive</code> with <code>parse</code> to:</p>
      <ul class="doc-list">
        <li>Decide whether fallback heuristics should run.</li>
        <li>Select which sections to keep.</li>
        <li>Rename sections before rendering.</li>
      </ul>

      <h2>Complex bundles: issues and mitigations</h2>
      <ul class="doc-list">
        <li>Ambiguous delimiters can cause false splits. Clinstruct-cli logs warnings and keeps the note intact when unsure.</li>
        <li>Mixed formats in a single file can map headings to the wrong target sections; interactive mode lets you confirm.</li>
        <li>Timestamp-only splits may fail when the same date appears inside a note; auto mode refuses weak splits.</li>
        <li>Heuristic headings can misclassify narrative text; you can disable heuristics or drop sections interactively.</li>
      </ul>

      <h2>Warnings</h2>
      <p>Warnings are serialized in JSON output and included in batch reports. They include codes, severity, and line spans.</p>
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