feat(explore): point at source this session already sent, don't send it twice (CG-18)

A later explore call re-served whatever it re-ranked, so on the #1500 report
the 4th call spent its envelope on the spine the 1st call had already
delivered. CG-17 recorded what was served; this acts on it.

What a withheld span becomes is the whole design: a POINTER, never a silence.
An insufficient-feeling response is what sends an agent to Read, and one or
two of those early in a session teach it to abandon codegraph — so the
replacement names the file, the symbols and the line spans, and says both
that the source came from THIS conversation and that the file has not changed
since.

- Content fingerprint, not the drift flag, gates it. They answer different
  questions: two calls inside one drift window served the same current bytes,
  while a file edited AND re-synced between calls is never "stale" and yet
  the agent's copy is now wrong. An edited file re-emits in full.
- Only a covered run of >= 8 lines is replaced, and a remainder under 160
  chars folds into the pointer. Below those the pointer costs more than the
  source and the block reads as shredded — a fence holding `228\t` is a
  broken-looking response, which is the expensive failure.
- The reclaimed bytes go to files the agent has NOT seen, two ways: a smaller
  `sourceSpent` hands slack down CG-21's carry-forward pool, and a fully
  back-referenced file gives up its maxFiles slot the way a cliffed one does.
  Within a file, the cluster shrink now reads the DEDUPED length, so it never
  drops new symbols to make room for source it isn't sending.
- If dedup suppresses everything and nothing new takes its place, the top
  suppressed file is spliced back in whole. An all-pointer response is the
  shape that reads as "codegraph found nothing"; one re-served file is the
  cheaper mistake.

Kill switch: CODEGRAPH_EXPLORE_DEDUP=0.

__tests__/explore-cross-call-dedup.test.ts

@@ -0,0 +1,360 @@
+/**
+ * Cross-call source dedup (CG-18).
+ *
+ * A later `codegraph_explore` call in a session must not re-send source an
+ * earlier call already delivered — but every byte it withholds has to be
+ * replaced by a POINTER, never a silence. That asymmetry is what this suite
+ * guards, because the two failure directions cost wildly different amounts: a
+ * duplicate range wastes a few thousand chars, while a response that reads as
+ * "codegraph doesn't have it" costs a Read — and one or two of those early in a
+ * session teach an agent to stop calling the tool at all.
+ *
+ * Three layers:
+ *   1. the range algebra — what is withheld, and the thresholds that stop it
+ *      from shredding a block into slivers;
+ *   2. the fingerprint gate — an edit between two calls must re-emit, since a
+ *      pointer to pre-edit source is worse than no dedup at all;
+ *   3. the handler seam — a real second call against a real index: no duplicate
+ *      ranges, a pointer for everything withheld, the reclaimed budget spent on
+ *      source the agent has NOT seen, and never an all-pointer response.
+ */
+import { describe, it, expect, beforeAll, afterAll } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import CodeGraph from '../src/index';
+import { ToolHandler } from '../src/mcp/tools';
+import { ExploreSessionState, type ExploreProjectState } from '../src/mcp/explore-session-state';
+import {
+  EXPLORE_DEDUP,
+  dedupeRange,
+  fileFingerprint,
+  formatBackReference,
+  intersectRange,
+  mergeRanges,
+  servedRangesForFile,
+  subtractRange,
+  symbolsInSpans,
+} from '../src/mcp/explore-dedup';
+
+const FIXTURE_SRC = path.join(__dirname, 'fixtures', 'payroll-go');
+const QUERY = 'how does payroll cycle create and calculate payslips?';
+const POINTER = 'Already sent earlier in this conversation';
+
+/** A prior-state shaped like the session tracker's, for the algebra tests. */
+function prior(files: Array<{ path: string; ranges: Array<[number, number]>; fingerprint?: string }>): ExploreProjectState {
+  return {
+    projectRoot: '/repo',
+    callCount: 1,
+    responseBytes: 1000,
+    calls: [{
+      index: 1,
+      projectRoot: '/repo',
+      query: 'q',
+      sourceBytes: 500,
+      responseBytes: 1000,
+      files: files.map((f) => ({
+        path: f.path,
+        ranges: f.ranges.map(([start, end]) => ({ start, end })),
+        bytes: 500,
+        fingerprint: f.fingerprint,
+      })),
+    }],
+  };
+}
+
+describe('range algebra', () => {
+  it('subtracts a held span out of the middle of an intended one', () => {
+    expect(subtractRange({ start: 1, end: 100 }, [{ start: 20, end: 40 }]))
+      .toEqual([{ start: 1, end: 19 }, { start: 41, end: 100 }]);
+  });
+
+  it('subtracts held spans at either edge, and a full cover to nothing', () => {
+    expect(subtractRange({ start: 10, end: 50 }, [{ start: 1, end: 20 }]))
+      .toEqual([{ start: 21, end: 50 }]);
+    expect(subtractRange({ start: 10, end: 50 }, [{ start: 30, end: 90 }]))
+      .toEqual([{ start: 10, end: 29 }]);
+    expect(subtractRange({ start: 10, end: 50 }, [{ start: 1, end: 90 }])).toEqual([]);
+  });
+
+  it('intersects to exactly what both sides hold', () => {
+    expect(intersectRange({ start: 10, end: 50 }, [{ start: 1, end: 20 }, { start: 45, end: 80 }]))
+      .toEqual([{ start: 10, end: 20 }, { start: 45, end: 50 }]);
+    expect(intersectRange({ start: 10, end: 50 }, [{ start: 60, end: 80 }])).toEqual([]);
+  });
+
+  it('merges touching spans — two adjacent blocks are one block of source', () => {
+    expect(mergeRanges([{ start: 5, end: 9 }, { start: 10, end: 12 }, { start: 40, end: 41 }]))
+      .toEqual([{ start: 5, end: 12 }, { start: 40, end: 41 }]);
+  });
+
+  it('emits ONLY the delta when a later call wants a wider window', () => {
+    // Call 1 sent the method; call 2 wants the class around it.
+    const { emit, covered } = dedupeRange({ start: 80, end: 200 }, [{ start: 100, end: 140 }]);
+    expect(covered).toEqual([{ start: 100, end: 140 }]);
+    expect(emit).toEqual([{ start: 80, end: 99 }, { start: 141, end: 200 }]);
+  });
+
+  it('withholds nothing when the overlap is smaller than a chunk worth pointing at', () => {
+    // Context padding and signature lines land here. Replacing them costs more
+    // in pointer text than the source is worth, and shreds the block.
+    const overlap = EXPLORE_DEDUP.MIN_COVERED_LINES - 1;
+    const { emit, covered } = dedupeRange({ start: 1, end: 100 }, [{ start: 10, end: 10 + overlap - 1 }]);
+    expect(covered).toEqual([]);
+    expect(emit).toEqual([{ start: 1, end: 100 }]);
+  });
+
+  it('leaves an untouched span exactly as it was', () => {
+    expect(dedupeRange({ start: 1, end: 50 }, [{ start: 200, end: 400 }]))
+      .toEqual({ emit: [{ start: 1, end: 50 }], covered: [] });
+    expect(dedupeRange({ start: 1, end: 50 }, []))
+      .toEqual({ emit: [{ start: 1, end: 50 }], covered: [] });
+  });
+});
+
+describe('the fingerprint gate', () => {
+  const FP = fileFingerprint('package main\nfunc main() {}\n');
+
+  it('returns the spans a call served for a file whose bytes are unchanged', () => {
+    const state = prior([{ path: 'a.go', ranges: [[1, 40], [60, 80]], fingerprint: FP }]);
+    expect(servedRangesForFile(state, 'a.go', FP)).toEqual([{ start: 1, end: 40 }, { start: 60, end: 80 }]);
+  });
+
+  it('returns NOTHING once the file has been edited — a pointer would be wrong', () => {
+    const state = prior([{ path: 'a.go', ranges: [[1, 40]], fingerprint: FP }]);
+    const edited = fileFingerprint('package main\nfunc main() { changed() }\n');
+    expect(servedRangesForFile(state, 'a.go', edited)).toEqual([]);
+  });
+
+  it('ignores a record that cannot prove what it served', () => {
+    const state = prior([{ path: 'a.go', ranges: [[1, 40]] }]);
+    expect(servedRangesForFile(state, 'a.go', FP)).toEqual([]);
+  });
+
+  it('never crosses files, and is empty for an untracked session', () => {
+    const state = prior([{ path: 'a.go', ranges: [[1, 40]], fingerprint: FP }]);
+    expect(servedRangesForFile(state, 'b.go', FP)).toEqual([]);
+    expect(servedRangesForFile(null, 'a.go', FP)).toEqual([]);
+  });
+
+  it('distinguishes two files that hash the same prefix but differ in length', () => {
+    expect(fileFingerprint('abc')).not.toBe(fileFingerprint('abcd'));
+    expect(fileFingerprint('abc')).toBe(fileFingerprint('abc'));
+  });
+});
+
+describe('the back-reference itself', () => {
+  const covered = [{ start: 100, end: 240 }];
+
+  it('names the file, the span and the symbols, and says the copy is still good', () => {
+    const text = formatBackReference('internal/x.go', covered, ['RunCycle', 'BuildPayslip'], { partial: false });
+    expect(text).toContain('internal/x.go');
+    expect(text).toContain('L100-240');
+    expect(text).toContain('RunCycle, BuildPayslip');
+    expect(text).toContain(POINTER);
+    expect(text).toContain('unchanged on disk');
+  });
+
+  it('never tells the agent to Read, in either shape', () => {
+    for (const partial of [true, false]) {
+      const text = formatBackReference('x.go', covered, ['A'], { partial });
+      expect(text).toMatch(/do NOT Read/i);
+      expect(text).not.toMatch(/\bRead (this|the) file (for|to)\b/i);
+      expect(text).not.toMatch(/omitted|unavailable|could not/i);
+    }
+  });
+
+  it('says the block below is only the NEW lines when the call still sends some', () => {
+    expect(formatBackReference('x.go', covered, [], { partial: true })).toContain('NEW lines');
+    expect(formatBackReference('x.go', covered, [], { partial: false })).toContain('not repeated here');
+  });
+
+  it('names only symbols that actually fall in the withheld spans', () => {
+    const nodes = [
+      { name: 'InSpan', kind: 'function', startLine: 110, endLine: 130 },
+      { name: 'Outside', kind: 'function', startLine: 300, endLine: 320 },
+      { name: 'AnImport', kind: 'import', startLine: 105, endLine: 105 },
+    ];
+    expect(symbolsInSpans(nodes, covered)).toEqual(['InSpan']);
+  });
+});
+
+describe('a second call against a real index', () => {
+  let testDir: string;
+  let cg: CodeGraph;
+  let handler: ToolHandler;
+
+  beforeAll(async () => {
+    testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-cg18-'));
+    fs.cpSync(FIXTURE_SRC, testDir, { recursive: true });
+    fs.rmSync(path.join(testDir, '.codegraph'), { recursive: true, force: true });
+    cg = CodeGraph.initSync(testDir);
+    await cg.indexAll();
+    handler = new ToolHandler(cg);
+  }, 120_000);
+
+  afterAll(() => {
+    if (cg) cg.destroy();
+    if (testDir && fs.existsSync(testDir)) fs.rmSync(testDir, { recursive: true, force: true });
+  });
+
+  const explore = (query: string, session?: ExploreSessionState, args: Record<string, unknown> = {}) =>
+    handler.execute('codegraph_explore', { query, ...args }, session).then((r) => r.content[0]!.text);
+
+  /**
+   * The line numbers actually inside each file's fenced source. Read off the
+   * RESPONSE, not the bookkeeping — "no duplicate ranges" is a claim about what
+   * the agent received, and checking it against the record we also wrote would
+   * prove only that the two agree.
+   */
+  function fencedLines(text: string): Map<string, Set<number>> {
+    const out = new Map<string, Set<number>>();
+    let current: string | null = null;
+    let inFence = false;
+    for (const line of text.split('\n')) {
+      const header = /^\*\*`([^`]+)`\*\*/.exec(line);
+      if (header && !inFence) { current = header[1]!; continue; }
+      if (!inFence && current && line.startsWith('```')) { inFence = true; continue; }
+      if (inFence && line === '```') { inFence = false; continue; }
+      if (!inFence || !current) continue;
+      const numbered = /^(\d+)\t/.exec(line);
+      if (!numbered) continue;
+      if (!out.has(current)) out.set(current, new Set());
+      out.get(current)!.add(Number(numbered[1]));
+    }
+    return out;
+  }
+
+  it('never re-sends a line it already sent, and points at every line it withholds', async () => {
+    const session = new ExploreSessionState();
+    const first = await explore(QUERY, session);
+    const second = await explore(QUERY, session);
+
+    const before = fencedLines(first);
+    const after = fencedLines(second);
+    expect(after.size).toBeGreaterThan(0);
+
+    // Every file whose source the second call withheld carries a pointer, and
+    // the pointer names it.
+    expect(second).toContain(POINTER);
+    for (const [file, lines] of before) {
+      const repeated = [...(after.get(file) ?? [])].filter((n) => lines.has(n));
+      if (repeated.length === 0) continue;
+      // The only sanctioned repeat is the anti-abandonment restore, which fires
+      // ONLY when the call found nothing new to say — and this one did.
+      throw new Error(`call 2 re-sent ${file} lines ${repeated.slice(0, 5).join(',')}`);
+    }
+  }, 120_000);
+
+  it('spends the reclaimed bytes on source the agent has not seen', async () => {
+    const session = new ExploreSessionState();
+    const first = await explore(QUERY, session);
+    const second = await explore(QUERY, session);
+
+    const before = fencedLines(first);
+    const after = fencedLines(second);
+    const fresh = [...after.entries()].reduce(
+      (sum, [file, lines]) => sum + [...lines].filter((n) => !(before.get(file)?.has(n))).length, 0);
+    // Not merely "smaller": a shrunken response is what dedup must NOT produce.
+    // The freed budget has to come back as lines the first call never sent.
+    expect(fresh).toBeGreaterThan(20);
+    expect(second.length).toBeLessThan(first.length);
+  }, 120_000);
+
+  it('re-emits in full when the file changed between the two calls', async () => {
+    const session = new ExploreSessionState();
+    const target = path.join(testDir, 'internal/usecase/payroll/payslip_builder.go');
+    const original = fs.readFileSync(target, 'utf-8');
+    try {
+      const first = await explore(QUERY, session);
+      expect(fencedLines(first).has('internal/usecase/payroll/payslip_builder.go')).toBe(true);
+
+      fs.writeFileSync(target, original.replace('func sumKind(', 'func sumKindRenamed('), 'utf-8');
+      const second = await explore(QUERY, session);
+
+      // The edited file is served again, whole — a pointer here would send the
+      // agent to a copy of the file that no longer exists.
+      const pointerLines = second.split('\n').filter((l) => l.includes(POINTER));
+      expect(pointerLines.some((l) => l.includes('payslip_builder.go'))).toBe(false);
+      expect(fencedLines(second).get('internal/usecase/payroll/payslip_builder.go')?.size ?? 0)
+        .toBeGreaterThan(20);
+    } finally {
+      fs.writeFileSync(target, original, 'utf-8');
+    }
+  }, 120_000);
+
+  it('always returns real source, even when the session already holds everything', async () => {
+    const session = new ExploreSessionState();
+    await explore(QUERY, session);
+    await explore(QUERY, session);
+    const third = await explore(QUERY, session);
+    const fourth = await explore(QUERY, session);
+
+    // An all-pointer response is the shape that reads as failure. Every call
+    // keeps at least one real fenced block, however much the session holds.
+    for (const [n, text] of [[3, third], [4, fourth]] as const) {
+      const lines = [...fencedLines(text).values()].reduce((s, set) => s + set.size, 0);
+      expect(lines, `call ${n} returned no source at all`).toBeGreaterThan(10);
+    }
+  }, 180_000);
+
+  it('leaves the first call of a session untouched', async () => {
+    const tracked = await explore(QUERY, new ExploreSessionState());
+    const untracked = await explore(QUERY);
+    expect(tracked).toBe(untracked);
+  }, 120_000);
+
+  it('keeps two sessions on one handler independent', async () => {
+    const a = new ExploreSessionState();
+    const b = new ExploreSessionState();
+    const firstForA = await explore(QUERY, a);
+    await explore(QUERY, a);
+    // B's first call has seen nothing, whatever A has been served.
+    expect(await explore(QUERY, b)).toBe(firstForA);
+  }, 180_000);
+
+  it('is off entirely under CODEGRAPH_EXPLORE_DEDUP=0', async () => {
+    const session = new ExploreSessionState();
+    const previous = process.env.CODEGRAPH_EXPLORE_DEDUP;
+    process.env.CODEGRAPH_EXPLORE_DEDUP = '0';
+    try {
+      const first = await explore(QUERY, session);
+      const second = await explore(QUERY, session);
+      expect(second).toBe(first);
+      expect(second).not.toContain(POINTER);
+    } finally {
+      if (previous === undefined) delete process.env.CODEGRAPH_EXPLORE_DEDUP;
+      else process.env.CODEGRAPH_EXPLORE_DEDUP = previous;
+    }
+  }, 120_000);
+
+  it('reports the reclaimed bytes through the CG-4 diagnostic', async () => {
+    const sidecar = path.join(testDir, 'cg18-diagnostic.jsonl');
+    const session = new ExploreSessionState();
+    const previous = process.env.CODEGRAPH_EXPLORE_DEBUG;
+    process.env.CODEGRAPH_EXPLORE_DEBUG = sidecar;
+    try {
+      await explore(QUERY, session);
+      await explore(QUERY, session);
+    } finally {
+      if (previous === undefined) delete process.env.CODEGRAPH_EXPLORE_DEBUG;
+      else process.env.CODEGRAPH_EXPLORE_DEBUG = previous;
+    }
+    const [one, two] = fs.readFileSync(sidecar, 'utf-8').trim().split('\n').map((l) => JSON.parse(l));
+
+    expect(one.dedup.savedChars).toBe(0);
+    expect(two.dedup.savedChars).toBeGreaterThan(1000);
+    expect(two.dedup.backReferenced.length).toBeGreaterThan(0);
+
+    // The reclamation is legible file by file: a back-referenced file spent
+    // none of its reservation, and the response still filled its envelope.
+    const backref = two.files.filter((f: { render: string }) => f.render === 'backref');
+    for (const f of backref) {
+      expect(f.emittedChars).toBe(0);
+      expect(f.dedupSavedChars).toBeGreaterThan(0);
+      expect(f.dedupCovered.length).toBeGreaterThan(0);
+    }
+    const spentOnFreshSource = two.files.reduce((s: number, f: { emittedChars: number }) => s + f.emittedChars, 0);
+    expect(spentOnFreshSource).toBeGreaterThan(0);
+  }, 120_000);
+});

src/mcp/explore-dedup.ts

@@ -0,0 +1,249 @@
+/**
+ * Cross-call source dedup for `codegraph_explore` (CG-18).
+ *
+ * The session record (CG-17) knows what earlier calls already sent. This module
+ * is the algebra that turns that record into a decision for the call being
+ * rendered: of the line ranges this call WOULD emit, which does the agent
+ * already hold, and what is genuinely new.
+ *
+ * Three rules shape everything here, and all three come from the same place —
+ * an insufficient-feeling response is what sends an agent to Read, and one or
+ * two of those early in a session teach it to abandon codegraph entirely
+ * (CLAUDE.md):
+ *
+ *   1. **A pointer, never a bare omission.** Removed source is replaced by a
+ *      back-reference naming the file, the symbols, and the line span, worded so
+ *      it is unmistakable that the source was already delivered IN THIS
+ *      CONVERSATION and is still current. Silence reads as "codegraph didn't
+ *      find it".
+ *   2. **Only prove-it dedup.** A span is withheld only when the file's bytes
+ *      are byte-identical to what was served (a content fingerprint, not an
+ *      mtime and not the index's drift flag). An edit between calls means the
+ *      agent's copy is wrong, so the source is re-emitted in full.
+ *   3. **Cut chunks, not slivers.** Only a covered run of at least
+ *      {@link EXPLORE_DEDUP.MIN_COVERED_LINES} lines is worth replacing. Below
+ *      that the pointer costs more than the source, and shattering a block into
+ *      one-line fragments produces exactly the ragged output that reads as a
+ *      failure. Everything not withheld is emitted — where the algebra is
+ *      unsure, it re-serves.
+ *
+ * Which way to be wrong, restated for this layer: re-serving something the agent
+ * has is a few hundred wasted chars; withholding something it never saw is a
+ * Read. Every threshold below leans to the first.
+ */
+
+import { createHash } from 'crypto';
+import type { ExploreLineRange, ExploreProjectState } from './explore-session-state';
+
+export const EXPLORE_DEDUP = {
+  /**
+   * Shortest already-served run that may be replaced by a back-reference.
+   *
+   * Sized against what dedup is actually FOR — a later call re-serving a whole
+   * method or file it already sent. A shorter covered run is either a signature
+   * line in a skeleton render or the ±3 lines of context padding around a
+   * cluster, and swapping either for a pointer trades bytes for noise: the
+   * pointer sentence is itself ~140 chars, so under this length dedup would
+   * make the response BIGGER while making it read as full of holes.
+   */
+  MIN_COVERED_LINES: 8,
+  /**
+   * Below this many chars of NEW source, a file's remainder is folded into its
+   * back-reference instead of being fenced on its own.
+   *
+   * The shape this exists for, seen on the CG-17 fixture: a third call whose
+   * only unheld line was the file's trailing blank one, rendered as a code fence
+   * containing `228\t`. A fence holding two lines of nothing reads as a broken
+   * response, and reading as broken is the expensive failure — it is the thing
+   * that sends an agent to Read and keeps it there. So a remainder this small is
+   * dropped rather than shown. It is the one place this module withholds
+   * something the agent has not seen, and it is bounded to ~two lines that sit
+   * directly against source the agent does hold; the file is still named, with
+   * its symbols, so one follow-up explore fetches it whole.
+   */
+  MIN_DELTA_CHARS: 160,
+  /** Line spans named in one pointer before it summarises the rest. */
+  MAX_SPANS_IN_POINTER: 4,
+  /** Symbols named in one pointer before it summarises the rest. */
+  MAX_SYMBOLS_IN_POINTER: 5,
+} as const;
+
+const OFF = new Set(['0', 'false', 'off', 'no']);
+
+/**
+ * Kill switch: `CODEGRAPH_EXPLORE_DEDUP=0` renders every call as if the session
+ * had no history. Read per call (not memoized) so a test can toggle it.
+ */
+export function exploreDedupEnabled(): boolean {
+  const raw = process.env.CODEGRAPH_EXPLORE_DEDUP;
+  if (raw === undefined) return true;
+  return !OFF.has(raw.trim().toLowerCase());
+}
+
+/**
+ * Identity of the bytes a call served for one file.
+ *
+ * This — not the index's drift flag — is what gates dedup. `isFileStaleOnDisk`
+ * answers "did the file change since the last INDEX SYNC", which is a different
+ * question with a different answer: two calls inside one drift window served the
+ * same current bytes (dedup is correct), while a file edited and re-synced
+ * between two calls is never "stale" and yet the agent's copy is now wrong
+ * (dedup would be actively harmful). Length is prefixed so a hash prefix
+ * collision cannot alias two files of different size.
+ */
+export function fileFingerprint(content: string): string {
+  return `${content.length}:${createHash('sha1').update(content).digest('hex').slice(0, 16)}`;
+}
+
+/** Sort + merge overlapping/adjacent spans into the smallest equivalent set. */
+export function mergeRanges(ranges: ReadonlyArray<ExploreLineRange>): ExploreLineRange[] {
+  const valid = ranges
+    .filter((r) => Number.isFinite(r.start) && Number.isFinite(r.end) && r.end >= r.start && r.start >= 1)
+    .map((r) => ({ start: Math.floor(r.start), end: Math.floor(r.end) }))
+    .sort((a, b) => a.start - b.start || a.end - b.end);
+  const out: ExploreLineRange[] = [];
+  for (const r of valid) {
+    const last = out[out.length - 1];
+    if (last && r.start <= last.end + 1) last.end = Math.max(last.end, r.end);
+    else out.push({ ...r });
+  }
+  return out;
+}
+
+/** The parts of `range` that `served` covers. */
+export function intersectRange(
+  range: ExploreLineRange,
+  served: ReadonlyArray<ExploreLineRange>,
+): ExploreLineRange[] {
+  const out: ExploreLineRange[] = [];
+  for (const s of served) {
+    const start = Math.max(range.start, s.start);
+    const end = Math.min(range.end, s.end);
+    if (end >= start) out.push({ start, end });
+  }
+  return mergeRanges(out);
+}
+
+/** The parts of `range` that `cut` does NOT cover. */
+export function subtractRange(
+  range: ExploreLineRange,
+  cut: ReadonlyArray<ExploreLineRange>,
+): ExploreLineRange[] {
+  const out: ExploreLineRange[] = [];
+  let cursor = range.start;
+  for (const c of mergeRanges(cut)) {
+    if (c.end < cursor) continue;
+    if (c.start > range.end) break;
+    if (c.start > cursor) out.push({ start: cursor, end: Math.min(c.start - 1, range.end) });
+    cursor = Math.max(cursor, c.end + 1);
+    if (cursor > range.end) break;
+  }
+  if (cursor <= range.end) out.push({ start: cursor, end: range.end });
+  return out;
+}
+
+/** What one intended span becomes once the session's history is applied. */
+export interface RangeDedup {
+  /** Spans to render now — everything not proven-already-held. */
+  emit: ExploreLineRange[];
+  /** Spans replaced by a back-reference. */
+  covered: ExploreLineRange[];
+}
+
+/**
+ * Split one intended span into what to emit and what to point back at.
+ *
+ * Covered runs shorter than {@link EXPLORE_DEDUP.MIN_COVERED_LINES} are left in
+ * the emit set on purpose (rule 3 above) — so a span the agent holds "almost
+ * all of" still comes back whole rather than as a stutter of fragments around
+ * pointers.
+ */
+export function dedupeRange(
+  range: ExploreLineRange,
+  served: ReadonlyArray<ExploreLineRange>,
+  minCovered: number = EXPLORE_DEDUP.MIN_COVERED_LINES,
+): RangeDedup {
+  if (served.length === 0 || range.end < range.start) return { emit: [range], covered: [] };
+  const covered = intersectRange(range, served).filter((r) => r.end - r.start + 1 >= minCovered);
+  if (covered.length === 0) return { emit: [range], covered: [] };
+  return { emit: subtractRange(range, covered), covered };
+}
+
+/**
+ * Every line span this session has already served for one file, but ONLY from
+ * calls that served the SAME BYTES.
+ *
+ * A record with no fingerprint is ignored rather than trusted: it cannot prove
+ * the agent's copy matches the file on disk now, and an unprovable match is
+ * exactly the case where re-serving is right.
+ */
+export function servedRangesForFile(
+  prior: ExploreProjectState | null,
+  filePath: string,
+  fingerprint: string,
+): ExploreLineRange[] {
+  if (!prior) return [];
+  const spans: ExploreLineRange[] = [];
+  for (const call of prior.calls) {
+    for (const file of call.files) {
+      if (file.path !== filePath) continue;
+      if (!file.fingerprint || file.fingerprint !== fingerprint) continue;
+      spans.push(...file.ranges);
+    }
+  }
+  return mergeRanges(spans);
+}
+
+/** `L12`, `L12-40`, capped with a `+N more` tail. */
+export function formatSpans(spans: ReadonlyArray<ExploreLineRange>): string {
+  const shown = spans.slice(0, EXPLORE_DEDUP.MAX_SPANS_IN_POINTER)
+    .map((r) => (r.start === r.end ? `L${r.start}` : `L${r.start}-${r.end}`))
+    .join(', ');
+  const more = spans.length - EXPLORE_DEDUP.MAX_SPANS_IN_POINTER;
+  return more > 0 ? `${shown}, +${more} more span${more === 1 ? '' : 's'}` : shown;
+}
+
+/**
+ * The line that replaces withheld source.
+ *
+ * It has one job: make the agent reach into its own context instead of into
+ * Read. So it carries the three things needed to find the source it already has
+ * — path, symbols, line spans — plus the two facts that make using it safe:
+ * that it came from THIS conversation, and that the file has not changed since
+ * (which is checked, not asserted — see {@link fileFingerprint}). It never says
+ * "omitted", and it never steers to Read.
+ */
+export function formatBackReference(
+  filePath: string,
+  covered: ReadonlyArray<ExploreLineRange>,
+  symbols: ReadonlyArray<string>,
+  opts: { partial: boolean },
+): string {
+  const names = symbols.slice(0, EXPLORE_DEDUP.MAX_SYMBOLS_IN_POINTER);
+  const moreNames = symbols.length - names.length;
+  const symbolPart = names.length > 0
+    ? ` (${names.join(', ')}${moreNames > 0 ? `, +${moreNames} more` : ''})`
+    : '';
+  const head = `> **Already sent earlier in this conversation:** \`${filePath}\` ${formatSpans(covered)}${symbolPart}`;
+  const tail = opts.partial
+    ? ' — unchanged on disk since, so that copy is still exact. Only the NEW lines are shown below; scroll back for the rest. Do NOT Read this file.'
+    : ' — unchanged on disk since, so that copy is still exact and is not repeated here. Use it from your context; do NOT Read this file.';
+  return head + tail;
+}
+
+/** Symbol names whose definitions fall inside the withheld spans. */
+export function symbolsInSpans(
+  nodes: ReadonlyArray<{ name: string; kind: string; startLine: number; endLine: number }>,
+  spans: ReadonlyArray<ExploreLineRange>,
+): string[] {
+  const out: string[] = [];
+  const seen = new Set<string>();
+  for (const n of nodes) {
+    if (n.kind === 'import' || n.kind === 'export') continue;
+    if (!spans.some((s) => n.startLine <= s.end && (n.endLine || n.startLine) >= s.start)) continue;
+    if (seen.has(n.name)) continue;
+    seen.add(n.name);
+    out.push(n.name);
+  }
+  return out;
+}

src/mcp/explore-diagnostics.ts

@@ -41,6 +41,7 @@ export type ExploreRenderMode =
   | 'focused'       // per-symbol view, named/spine bodies full
   | 'skeleton'      // per-symbol view, signatures only
   | 'stale-omitted' // drifted on disk; source deliberately withheld
+  | 'backref'       // fully served by an earlier call this session (CG-18)
   | 'dropped';      // rendered into `lines` but cut by the final hard ceiling
 
 /** Why a ranked candidate never reached the output. */
@@ -92,6 +93,17 @@ interface FileRecord extends ExploreCandidateMeta {
    */
   allowance: number | null;
   render?: ExploreRenderMode;
+  /**
+   * Source chars this call did NOT re-send because an earlier call in the
+   * session already did (CG-18). Reclaimed, not lost: it leaves through
+   * `sourceSpent` (the carry-forward pool hands it to lower-ranked files) and,
+   * for a fully back-referenced file, through the freed `maxFiles` slot. The
+   * reallocation is legible as the difference between this file's
+   * `allowance` and `emittedChars` against the files below it in the table.
+   */
+  dedupSavedChars: number;
+  /** Line spans replaced by a back-reference. */
+  dedupCovered: Array<[number, number]>;
   /** Source chars the render loop handed to `lines` (pre-final-truncation). */
   emittedChars: number;
   /** Source chars present in the FINAL text — authoritative, truncation-aware. */
@@ -130,6 +142,8 @@ export interface ExploreDiagnosticFile extends ExploreCandidateMeta {
   render: ExploreRenderMode | null;
   skipped: ExploreSkipReason | null;
   clipped: boolean;
+  dedupSavedChars: number;
+  dedupCovered: Array<[number, number]>;
   emittedChars: number;
   finalChars: number;
   share: number;
@@ -191,6 +205,17 @@ export interface ExploreDiagnosticReport {
     filesRenderedByLoop: number;
     filesInFinalOutput: number;
   };
+  /**
+   * Cross-call source dedup (CG-18): what this call did NOT re-send because an
+   * earlier call in this session already sent it, and where those bytes went.
+   * `savedChars` 0 with a non-empty session block means nothing overlapped.
+   */
+  dedup: {
+    savedChars: number;
+    backReferenced: string[];
+    /** Files fully replaced by a pointer — each one also freed a `maxFiles` slot. */
+    fullyBackReferenced: string[];
+  };
   /** The proportional split (CG-12): what each file was promised, and why. */
   allocation: {
     /** Chars divided among admitted files (envelope minus per-file overhead). */
@@ -338,6 +363,7 @@ export class ExploreDiagnostics {
   noteCandidate(path: string, meta: ExploreCandidateMeta): void {
     this.files.set(path, {
       path, ...meta, allowance: null,
+      dedupSavedChars: 0, dedupCovered: [],
       emittedChars: 0, finalChars: 0, share: 0, allocatedShare: 0, clipped: false,
     });
   }
@@ -375,6 +401,19 @@ export class ExploreDiagnostics {
     rec.skipped = undefined;
   }
 
+  /**
+   * Source this call withheld because the session already holds it (CG-18).
+   * Called with `(path, 0, [])` to clear a record — the anti-abandonment restore
+   * puts a suppressed file's source back, and a diagnostic still claiming the
+   * saving would misreport where the envelope went.
+   */
+  recordDedup(path: string, savedChars: number, covered: ReadonlyArray<{ start: number; end: number }>): void {
+    const rec = this.files.get(path);
+    if (!rec) return;
+    rec.dedupSavedChars = savedChars;
+    rec.dedupCovered = covered.map((r) => [r.start, r.end] as [number, number]);
+  }
+
   /**
    * A candidate was passed over before rendering. First reason wins — the
    * blanket `max-files` sweep must not overwrite a file's specific reason.
@@ -410,8 +449,10 @@ export class ExploreDiagnostics {
         rec.share = envelope > 0 ? rec.finalChars / envelope : 0;
         rec.allocatedShare = allocatedChars > 0 ? rec.emittedChars / allocatedChars : 0;
         // Rendered into `lines` but absent from the final text → the hard
-        // ceiling dropped its whole section.
-        if (rec.render && rec.render !== 'stale-omitted' && rec.finalChars === 0) {
+        // ceiling dropped its whole section. A back-referenced file has no
+        // fenced source BY DESIGN (CG-18), so it is never "dropped".
+        if (rec.render && rec.render !== 'stale-omitted' && rec.render !== 'backref'
+            && rec.finalChars === 0) {
           rec.render = 'dropped';
           rec.clipped = true;
         }
@@ -467,6 +508,11 @@ export class ExploreDiagnostics {
         filesRenderedByLoop: filesIncluded,
         filesInFinalOutput: rendered.length,
       },
+      dedup: {
+        savedChars: records.reduce((s, r) => s + r.dedupSavedChars, 0),
+        backReferenced: records.filter((r) => r.dedupSavedChars > 0).map((r) => r.path),
+        fullyBackReferenced: records.filter((r) => r.render === 'backref').map((r) => r.path),
+      },
       allocation: {
         pool: this.allocPool,
         cliffAt: round6(this.allocCliffAt),
@@ -495,6 +541,8 @@ export class ExploreDiagnostics {
           render: r.render ?? null,
           skipped: r.skipped ?? null,
           clipped: r.clipped,
+          dedupSavedChars: r.dedupSavedChars,
+          dedupCovered: r.dedupCovered.map((s) => [...s] as [number, number]),
           emittedChars: r.emittedChars,
           finalChars: r.finalChars,
           share: round6(r.share),
@@ -614,6 +662,15 @@ export function renderTable(report: ExploreDiagnosticReport): string {
     `  relevance gate ${sel.graphGateApplied ? 'applied' : 'not applied'}` +
     ` at graph >= ${sel.graphGateThreshold.toFixed(5)} (6% of max ${sel.maxGraph.toFixed(5)})`,
   );
+  const dedup = report.dedup;
+  if (dedup && dedup.savedChars > 0) {
+    out.push(
+      `  dedup ${num(dedup.savedChars)} chars not re-sent` +
+      ` · ${dedup.fullyBackReferenced.length} file(s) fully back-referenced` +
+      ` (each also freed a maxFiles slot)` +
+      (dedup.backReferenced.length > 0 ? `: ${dedup.backReferenced.join(', ')}` : ''),
+    );
+  }
   const alloc = report.allocation;
   out.push(
     `  allocation ${num(alloc.reserved)} reserved of ${num(alloc.pool)} pool` +
@@ -627,7 +684,7 @@ export function renderTable(report: ExploreDiagnosticReport): string {
   // Allocated (not delivered) is the allocator's own decision — the number the
   // budget work is about. Delivered is what the agent got. They differ only
   // when the ceiling truncated; showing both makes that divergence obvious.
-  const shown = files.filter((f) => f.emittedChars > 0 || f.finalChars > 0);
+  const shown = files.filter((f) => f.emittedChars > 0 || f.finalChars > 0 || f.render === 'backref');
   if (shown.length > 0) {
     out.push('   #  alloc%  deliv%    bytes  reserved  score    graph  hits  pen   flags                render     file');
     for (const f of shown) {
@@ -647,6 +704,11 @@ export function renderTable(report: ExploreDiagnosticReport): string {
         f.path,
       );
       out.push('        kinds: ' + (f.kinds || '-'));
+      if (f.dedupSavedChars > 0) {
+        const spans = f.dedupCovered.slice(0, 6).map(([a, b]) => (a === b ? `${a}` : `${a}-${b}`)).join(',');
+        const more = f.dedupCovered.length > 6 ? `,+${f.dedupCovered.length - 6}` : '';
+        out.push(`        dedup: ${num(f.dedupSavedChars)} chars already sent this session · L${spans}${more}`);
+      }
     }
     out.push('  (bytes = source allocated by the render loop; deliv% = 0 means the hard ceiling dropped the section)');
     out.push('  (* = clipped: some source in this file was elided, windowed, or its section dropped)');

src/mcp/explore-session-state.ts

@@ -70,6 +70,13 @@ export interface ExploreFileEmission {
   ranges: ExploreLineRange[];
   /** Source chars emitted for this file (excludes headers / fences). */
   bytes: number;
+  /**
+   * Identity of the bytes those ranges were sliced from (CG-18). Cross-call
+   * dedup withholds a span only when the file still hashes to this, so an edit
+   * between two calls re-serves instead of pointing at source the agent holds a
+   * now-wrong copy of. Absent = unprovable, which dedup treats as "re-serve".
+   */
+  fingerprint?: string;
   /** Set when ranges were dropped to stay under the per-file bound. */
   rangesTruncated?: boolean;
 }
@@ -309,6 +316,7 @@ export class ExploreSessionState {
       .map((f) => {
         const { ranges, truncated } = coalesceRanges(f.ranges ?? []);
         const out: ExploreFileEmission = { path: f.path, ranges, bytes: Math.max(0, f.bytes || 0) };
+        if (typeof f.fingerprint === 'string' && f.fingerprint) out.fingerprint = f.fingerprint;
         if (truncated) out.rangesTruncated = true;
         return out;
       });

src/mcp/server-instructions.ts

@@ -62,6 +62,8 @@ calls; a grep/read exploration is dozens.
 - **After editing, check the staleness banner.** When a tool response starts with "⚠️ Some files referenced below were edited since the last index sync…", the listed files are pending re-index — Read those specific files for accurate content. Every file NOT in that banner is fresh, so still trust codegraph. A different, rarer banner — "⚠️ CodeGraph auto-sync is DISABLED…" — means live watching stopped entirely (the whole index is frozen, not just a few files); until it's resolved, Read files directly to confirm anything that may have changed.
 - **A file flagged "⚠ changed on disk after the last index sync" drifted from its index** (most common on projects queried via \`projectPath\`, which have no live watcher). Codegraph never serves a possibly-mis-sliced body from such a file — it either shows the file's full CURRENT source (trust it as a Read) or omits the source with this flag. When the source was omitted, Read that specific file; line numbers referencing it elsewhere in the response may be shifted until that project's next sync. All unflagged files remain trustworthy.
 
+- **"Already sent earlier in this conversation" is a pointer, not a gap.** When a file's section carries that line instead of (or above) its source, an earlier \`codegraph_explore\` in THIS conversation already returned those exact lines and the file has not changed since — so the copy already in your context is current and exact. Scroll back to it; don't re-fetch it and don't Read the file. The bytes it freed went into source you have not seen yet, elsewhere in the same response.
+
 ## Limitations
 
 - If a tool reports a project isn't indexed (no \`.codegraph/\`), stop calling codegraph tools for that project for the rest of the session and use your built-in tools there instead. Indexing is the user's decision — mention they can run \`codegraph init\` if it comes up, but don't run it yourself.

src/mcp/tools.ts

@@ -52,6 +52,16 @@ import {
   type ExploreFileEmission,
   type ExploreLineRange,
 } from './explore-session-state';
+import {
+  EXPLORE_DEDUP,
+  dedupeRange,
+  exploreDedupEnabled,
+  fileFingerprint,
+  formatBackReference,
+  mergeRanges,
+  servedRangesForFile,
+  symbolsInSpans,
+} from './explore-dedup';
 
 /**
  * An expected, recoverable "codegraph can't serve this" condition — most
@@ -3120,26 +3130,50 @@ export class ToolHandler {
     // byte-identical. It only OBSERVES: it must never feed back into rendering.
     const diag = ExploreDiagnostics.start(query, projectRoot, budget, maxFiles, indexedFileCount);
 
-    // What this session has already been served for THIS project (CG-17).
-    // Read-only at this stage — it is reported in the diagnostic and nothing
-    // else, so the response is unchanged. Cross-call dedup (CG-18) and budget
-    // decay (CG-19) are the consumers this exists for.
+    // What this session has already been served for THIS project (CG-17), and
+    // whether this call may act on it (CG-18). Dedup is off on the session's
+    // first call by construction — there is nothing to point back AT — and off
+    // entirely under `CODEGRAPH_EXPLORE_DEDUP=0`.
     const priorCalls = viewForProject(readExploreSessionView(args), projectRoot);
     diag?.noteSession(priorCalls);
+    const dedupEnabled = exploreDedupEnabled() && (priorCalls?.calls.length ?? 0) > 0;
+
+    // Cross-call dedup accounting (CG-18). `newSourceChars` is the load-bearing
+    // one: a response whose source is ENTIRELY back-references is the shape that
+    // reads as a failure, so the loop keeps the top suppressed file's real
+    // section in hand and restores it if nothing new made it in — see
+    // `suppressedFallback` below.
+    let newSourceChars = 0;
+    const backReferencedFiles: string[] = [];
 
     // What this call ends up emitting, per file — the record handed back to the
     // session state on the main thread. Filled by every render path below, then
     // filtered to the files that SURVIVE the final hard-ceiling cut, so the
     // record is what the agent actually received rather than what the loop
     // hoped to send.
-    const emittedByFile = new Map<string, { ranges: ExploreLineRange[]; bytes: number }>();
-    const noteEmitted = (fp: string, ranges: ExploreLineRange[], bytes: number): void => {
+    //
+    // Back-referenced spans are recorded too, with zero bytes (CG-18): the
+    // record means "source the agent HOLDS for this file", not "bytes this call
+    // spent". Re-recording them refreshes them inside the retained-call window,
+    // so a file pointed at across many calls doesn't age out of the history and
+    // get re-served for no reason.
+    const emittedByFile = new Map<
+      string,
+      { ranges: ExploreLineRange[]; bytes: number; fingerprint?: string }
+    >();
+    const noteEmitted = (
+      fp: string,
+      ranges: ExploreLineRange[],
+      bytes: number,
+      fingerprint?: string,
+    ): void => {
       const existing = emittedByFile.get(fp);
       if (existing) {
         existing.ranges.push(...ranges);
         existing.bytes += bytes;
+        if (fingerprint) existing.fingerprint = fingerprint;
       } else {
-        emittedByFile.set(fp, { ranges: [...ranges], bytes });
+        emittedByFile.set(fp, { ranges: [...ranges], bytes, fingerprint });
       }
     };
 
@@ -3976,6 +4010,28 @@ export class ToolHandler {
     // instead of a different symbol's code under the requested name.
     const staleRendered: string[] = [];
     const staleOmitted: string[] = [];
+    // Anti-abandonment hold-back (CG-18). The first file dedup suppressed
+    // ENTIRELY, kept with its real section so it can be put back if the loop
+    // ends with no new source anywhere. A response made only of pointers is the
+    // shape that reads as "codegraph has nothing" — and one such response early
+    // in a session is enough to make an agent stop calling the tool at all — so
+    // the highest-ranked suppressed file is restored rather than risk it. It
+    // costs a re-serve of one file, on the one call shape where dedup would
+    // otherwise have saved everything: the safe direction.
+    type SuppressedFallback = {
+      filePath: string;
+      /** Index in `lines` where this file's pointer block starts. */
+      at: number;
+      /** How many `lines` entries the pointer block occupies. */
+      replacing: number;
+      /** The full, undeduped section to splice back in. */
+      section: string[];
+      sourceChars: number;
+      overhead: number;
+      ranges: ExploreLineRange[];
+      fingerprint: string;
+    };
+    let suppressedFallback: SuppressedFallback | null = null;
     // Reservation carry-forward (CG-21). A reservation is a promise the render
     // loop has to KEEP, not a cap it may quietly under-use: a file that cannot
     // spend what it was given — thin matched-symbol set, unreadable, drifted off
@@ -4053,6 +4109,135 @@ export class ToolHandler {
 
       const fileLines = fileContent.split('\n');
       const lang = group.nodes[0]?.language || '';
+      const withLineNumbers = exploreLineNumbersEnabled();
+      // Language-neutral separator between two non-contiguous slices of one file
+      // (no `//` — not a comment in Python, Ruby, etc.). With line numbers on,
+      // the line-number jump also signals the gap.
+      const GAP_MARKER = '\n\n... (gap) ...\n\n';
+
+      // Cross-call dedup (CG-18). `served` is what THIS session already sent the
+      // agent for THIS file, and it is empty unless the file still hashes to the
+      // bytes those spans were sliced from — an edit between calls means the
+      // agent's copy is wrong, so nothing is withheld. Every render path below
+      // routes its spans through `dedupeSpans`, which is the only place a span
+      // is ever dropped.
+      const fingerprint = fileFingerprint(fileContent);
+      const served = dedupEnabled ? servedRangesForFile(priorCalls, filePath, fingerprint) : [];
+      /** Render one line span exactly as the render paths do. */
+      const renderSpan = (r: ExploreLineRange): string => {
+        const slice = fileLines.slice(r.start - 1, r.end).join('\n');
+        return withLineNumbers ? numberSourceLines(slice, r.start) : slice;
+      };
+      /**
+       * Apply the session history to a set of spans-with-text. A span the agent
+       * already holds is dropped and reported in `covered`; a partially-held one
+       * is re-rendered down to its new lines. Text is rebuilt from the surviving
+       * spans rather than sliced out of the original string — the spans ARE the
+       * contract with the session record, so rebuilding from them is what keeps
+       * what we claim to have sent and what we sent the same thing.
+       */
+      const dedupeSpans = (
+        parts: ReadonlyArray<{ range: ExploreLineRange; text: string }>,
+      ): { parts: Array<{ range: ExploreLineRange; text: string }>; covered: ExploreLineRange[] } => {
+        if (served.length === 0) return { parts: [...parts], covered: [] };
+        const kept: Array<{ range: ExploreLineRange; text: string }> = [];
+        const covered: ExploreLineRange[] = [];
+        for (const part of parts) {
+          const split = dedupeRange(part.range, served);
+          if (split.covered.length === 0) {
+            kept.push(part);
+            continue;
+          }
+          covered.push(...split.covered);
+          for (const r of split.emit) kept.push({ range: r, text: renderSpan(r) });
+        }
+        return { parts: kept, covered: mergeRanges(covered) };
+      };
+      const coveredChars = (spans: ReadonlyArray<ExploreLineRange>): number =>
+        spans.reduce((sum, r) => sum + fileLines.slice(r.start - 1, r.end).join('\n').length, 0);
+      /**
+       * Emit one file's section — header, the back-reference for whatever the
+       * agent already holds, and the fence for what is new. Every render path
+       * ends here so that the dedup bookkeeping (freed bytes, freed `maxFiles`
+       * slot, the session record, the diagnostic) is written in exactly one
+       * place and no path can forget a piece of it.
+       *
+       * A fully-held file emits its header and pointer and NO fence, and
+       * deliberately does not consume a `maxFiles` slot: that is half of where
+       * the reclaimed budget goes (the other half is `sourceSpent`, which the
+       * carry-forward pool hands down the rank order). Both send bytes to files
+       * the agent has NOT seen, which is the whole point.
+       */
+      const emitFileSection = (opts: {
+        header: string;
+        /** Deduped source. Empty ⇒ the agent already holds all of it. */
+        body: string;
+        /** Spans `body` covers. */
+        ranges: ExploreLineRange[];
+        /** Spans replaced by the back-reference. */
+        covered: ExploreLineRange[];
+        /** Chars charged to `totalChars` on top of the body (fences, header). */
+        overhead: number;
+        mode: 'whole' | 'clusters' | 'focused' | 'skeleton';
+        clipped: boolean;
+        /** The undeduped render, kept for the no-new-source fallback. */
+        fullBody: string;
+        fullRanges: ExploreLineRange[];
+      }): void => {
+        // A remainder too small to be worth a fence is folded into the pointer
+        // (see MIN_DELTA_CHARS). Its ranges are then NOT recorded — the record
+        // must only ever claim source that was actually sent.
+        const folded = opts.covered.length > 0 && opts.body.length < EXPLORE_DEDUP.MIN_DELTA_CHARS;
+        const body = folded ? '' : opts.body;
+        const ranges = folded ? [] : opts.ranges;
+        const at = lines.length;
+        lines.push(opts.header, '');
+        if (opts.covered.length > 0) {
+          const pointer = formatBackReference(
+            filePath,
+            opts.covered,
+            symbolsInSpans(group.nodes, opts.covered),
+            { partial: body.length > 0 },
+          );
+          lines.push(pointer, '');
+          totalChars += pointer.length + 2;
+          backReferencedFiles.push(filePath);
+        }
+        if (body.length > 0) {
+          lines.push('```' + lang, body, '```', '');
+          totalChars += body.length + opts.overhead;
+          sourceSpent += body.length;
+          newSourceChars += body.length;
+          diag?.recordRender(filePath, opts.mode, body.length, opts.clipped || opts.covered.length > 0);
+          if (opts.covered.length > 0) diag?.recordDedup(filePath, coveredChars(opts.covered), opts.covered);
+          noteEmitted(filePath, [...ranges, ...opts.covered], body.length, fingerprint);
+          renderedFilePaths.push(filePath);
+          filesIncluded++;
+          return;
+        }
+        // Fully held. The section is the pointer; the slot and the bytes go to a
+        // file the agent has not seen. The spans are still recorded (at zero
+        // bytes) because the record means "source the agent HAS", not "bytes
+        // this call spent" — refreshing them keeps a long session from ageing
+        // them out of the retained window and re-serving them for nothing.
+        totalChars += opts.overhead;
+        diag?.recordRender(filePath, 'backref', 0, false);
+        diag?.recordDedup(filePath, coveredChars(opts.covered), opts.covered);
+        noteEmitted(filePath, opts.covered, 0, fingerprint);
+        renderedFilePaths.push(filePath);
+        if (!suppressedFallback && opts.fullBody.length > 0) {
+          suppressedFallback = {
+            filePath,
+            at,
+            replacing: lines.length - at,
+            section: [opts.header, '', '```' + lang, opts.fullBody, '```', ''],
+            sourceChars: opts.fullBody.length,
+            overhead: opts.overhead,
+            ranges: opts.fullRanges,
+            fingerprint,
+          };
+        }
+      };
 
       // Disk-drift gate (#1474): every render branch below except whole-file
       // slices fileContent (CURRENT bytes) at INDEXED line ranges. Content is
@@ -4132,8 +4317,7 @@ export class ToolHandler {
         // Pass 2: render in line order — full body for chosen symbols, else the
         // signature line (capped, with a "+N more" tail so the structure map of a
         // god-file doesn't itself bloat the budget).
-        const skel: string[] = [];
-        const skelRanges: ExploreLineRange[] = [];
+        const skel: Array<{ range: ExploreLineRange; text: string }> = [];
         let coveredUntil = 0; // skip symbols already inside an emitted body
         let sigCount = 0, sigDropped = 0;
         const SIG_MAX = Math.max(12, budget.maxSymbolsInFileHeader * 2);
@@ -4142,8 +4326,10 @@ export class ToolHandler {
           if (bodyIds.has(n.id)) {
             const end = n.endLine;
             const body = fileLines.slice(n.startLine - 1, end).join('\n');
-            skel.push(exploreLineNumbersEnabled() ? numberSourceLines(body, n.startLine) : body);
-            skelRanges.push({ start: n.startLine, end });
+            skel.push({
+              range: { start: n.startLine, end },
+              text: withLineNumbers ? numberSourceLines(body, n.startLine) : body,
+            });
             coveredUntil = end;
           } else {
             // Elide the body, emit the signature. node.startLine can point at a
@@ -4156,13 +4342,15 @@ export class ToolHandler {
             if (sigCount >= SIG_MAX) { sigDropped++; continue; }
             const sig = (fileLines[lineNo - 1] || '').trim();
             if (sig) {
-              skel.push(exploreLineNumbersEnabled() ? `${lineNo}\t${sig}` : sig);
-              skelRanges.push({ start: lineNo, end: lineNo });
+              skel.push({
+                range: { start: lineNo, end: lineNo },
+                text: withLineNumbers ? `${lineNo}\t${sig}` : sig,
+              });
               sigCount++;
             }
           }
         }
-        if (sigDropped > 0) skel.push(`… +${sigDropped} more (signatures elided)`);
+        const sigTail = sigDropped > 0 ? `… +${sigDropped} more (signatures elided)` : '';
         if (skel.length > 0) {
           const names = [...new Set(group.nodes.filter(n => n.kind !== 'import' && n.kind !== 'export').map(n => n.name))]
             .slice(0, budget.maxSymbolsInFileHeader).join(', ');
@@ -4175,14 +4363,25 @@ export class ToolHandler {
           const tag = bodyIds.size > 0
             ? 'focused (the methods you named in full, the rest as signatures — codegraph_explore a signature by name for its body; do NOT Read)'
             : 'skeleton (signatures only — codegraph_explore a name for its full body; do NOT Read)';
-          lines.push(fileSectionHeader(filePath, `${names} · ${tag}`), '', '```' + lang, skel.join('\n'), '```', '');
-          totalChars += skel.join('\n').length + 120;
-          sourceSpent += skel.join('\n').length;
-          // Always "clipped": the per-symbol view elides bodies by construction.
-          diag?.recordRender(filePath, bodyIds.size > 0 ? 'focused' : 'skeleton', skel.join('\n').length, true);
-          noteEmitted(filePath, skelRanges, skel.join('\n').length);
-          renderedFilePaths.push(filePath);
-          filesIncluded++;
+          // Dedup runs on the per-symbol parts, so a body the agent already has
+          // becomes a pointer while the signature map around it survives intact
+          // (a one-line signature is far under MIN_COVERED_LINES and is never
+          // withheld — the structure map is what makes this render legible).
+          const dd = dedupeSpans(skel);
+          const withTail = (parts: ReadonlyArray<{ text: string }>) =>
+            [...parts.map((p) => p.text), ...(sigTail ? [sigTail] : [])].join('\n');
+          emitFileSection({
+            header: fileSectionHeader(filePath, `${names} · ${tag}`),
+            body: dd.parts.length > 0 ? withTail(dd.parts) : '',
+            ranges: dd.parts.map((p) => p.range),
+            covered: dd.covered,
+            overhead: 120,
+            mode: bodyIds.size > 0 ? 'focused' : 'skeleton',
+            // Always "clipped": the per-symbol view elides bodies by construction.
+            clipped: true,
+            fullBody: withTail(skel),
+            fullRanges: skel.map((p) => p.range),
+          });
           continue;
         }
       }
@@ -4260,7 +4459,14 @@ export class ToolHandler {
             && totalChars + fileContent.length + EXPLORE_ALLOCATION.FILE_OVERHEAD <= renderCeiling);
       if (fileLines.length <= WHOLE_FILE_MAX_LINES && buysWhole) {
         const body = fileContent.replace(/\n+$/, '');
-        let wholeSection = exploreLineNumbersEnabled() ? numberSourceLines(body, 1) : body;
+        const wholeRange: ExploreLineRange = { start: 1, end: body.split('\n').length };
+        const fullSection = withLineNumbers ? numberSourceLines(body, 1) : body;
+        // The buy decision above was made on the file's FULL size on purpose: it
+        // asks "did this file's relevance earn all of itself", which dedup does
+        // not change. Dedup then only ever makes the render smaller, so a buy
+        // that was funded stays funded.
+        const ddWhole = dedupeSpans([{ range: wholeRange, text: fullSection }]);
+        const wholeSection = ddWhole.parts.map((p) => p.text).join(GAP_MARKER);
         const uniqSymbols = [...new Set(
           group.nodes
             .filter(n => n.kind !== 'import' && n.kind !== 'export')
@@ -4281,14 +4487,18 @@ export class ToolHandler {
           diag?.recordSkip(filePath, 'budget-whole-file');
           continue;
         }
-        lines.push(wholeHeader, '', '```' + lang, wholeSection, '```', '');
-        totalChars += wholeSection.length + 200;
-        sourceSpent += wholeSection.length;
-        diag?.recordRender(filePath, 'whole', wholeSection.length, false);
-        // The whole file, minus any trailing blank lines the render trimmed.
-        noteEmitted(filePath, [{ start: 1, end: body.split('\n').length }], wholeSection.length);
-        renderedFilePaths.push(filePath);
-        filesIncluded++;
+        emitFileSection({
+          header: wholeHeader,
+          body: wholeSection,
+          // The whole file, minus any trailing blank lines the render trimmed.
+          ranges: ddWhole.parts.map((p) => p.range),
+          covered: ddWhole.covered,
+          overhead: 200,
+          mode: 'whole',
+          clipped: false,
+          fullBody: fullSection,
+          fullRanges: [wholeRange],
+        });
         if (fileStale) staleRendered.push(filePath);
         continue;
       }
@@ -4441,10 +4651,6 @@ export class ToolHandler {
       // until the per-file char cap is hit. Truly enormous single clusters
       // get tail-trimmed with a marker.
       const contextPadding = 3;
-      const withLineNumbers = exploreLineNumbersEnabled();
-      // Language-neutral separator (no `//` — not a comment in Python, Ruby,
-      // etc.). With line numbers on, the line-number jump also signals the gap.
-      const GAP_MARKER = '\n\n... (gap) ...\n\n';
       // An oversize spine method (the call path runs THROUGH a god-method — n8n's
       // processRunExecutionData is 962 lines) is windowed to its next-hop CALL site
       // plus the signature head, NOT dumped whole. Without this the cluster is too big
@@ -4453,42 +4659,50 @@ export class ToolHandler {
       // the spine's call still appears in context.
       const OVERSIZE_SPINE_LINES = 200;
       const SPINE_WINDOW = 28; // lines each side of the next-hop call site
-      // Returns the rendered text AND the line spans it covers. The spans are
-      // what the session record is built from (CG-17): reporting them from the
-      // same function that slices the source is what keeps the record honest —
-      // a second function mirroring these window/padding rules would drift, and
-      // a record that claims lines it never sent withholds them from a later
-      // call, which costs a Read.
+      // Returns the rendered text as SPAN-KEYED PARTS. Every part carries the
+      // exact line range its text was sliced from, which two things depend on:
+      // the session record (CG-17) — a record claiming lines it never sent would
+      // withhold them from a later call, costing a Read — and cross-call dedup
+      // (CG-18), which rebuilds a part's text from a narrower span when the
+      // agent already holds the rest. Both read the spans from the function that
+      // does the slicing; a second function mirroring these window/padding rules
+      // would drift.
+      type SectionPart = { range: ExploreLineRange; text: string };
+      const sectionText = (parts: ReadonlyArray<SectionPart>): string =>
+        parts.map((p) => p.text).join(GAP_MARKER);
       const buildSection = (
         c: { start: number; end: number; hasSpine?: boolean; spineCallLine?: number },
-      ): { text: string; ranges: ExploreLineRange[] } => {
+      ): SectionPart[] => {
         if (c.hasSpine && c.spineCallLine && (c.end - c.start + 1) > OVERSIZE_SPINE_LINES) {
           const call = c.spineCallLine;
           const winStart = Math.max(c.start, call - SPINE_WINDOW);
           const winEnd = Math.min(c.end, call + SPINE_WINDOW);
-          const parts: string[] = [];
-          const spans: ExploreLineRange[] = [];
+          const parts: SectionPart[] = [];
           // Signature head, only when it sits clearly above the window (else the
           // window already covers the method opening).
           const headEnd = Math.min(c.start + 4, winStart - 2);
           if (headEnd >= c.start) {
             const head = fileLines.slice(c.start - 1, headEnd).join('\n');
-            parts.push(withLineNumbers ? numberSourceLines(head, c.start) : head);
-            spans.push({ start: c.start, end: headEnd });
+            parts.push({
+              range: { start: c.start, end: headEnd },
+              text: withLineNumbers ? numberSourceLines(head, c.start) : head,
+            });
           }
           const win = fileLines.slice(winStart - 1, winEnd).join('\n');
-          parts.push(withLineNumbers ? numberSourceLines(win, winStart) : win);
-          spans.push({ start: winStart, end: winEnd });
-          return { text: parts.join(GAP_MARKER), ranges: spans };
+          parts.push({
+            range: { start: winStart, end: winEnd },
+            text: withLineNumbers ? numberSourceLines(win, winStart) : win,
+          });
+          return parts;
         }
         const startIdx = Math.max(0, c.start - 1 - contextPadding);
         const endIdx = Math.min(fileLines.length, c.end + contextPadding);
         const slice = fileLines.slice(startIdx, endIdx).join('\n');
         // startIdx is 0-based, so the slice's first line is line startIdx + 1.
-        return {
+        return [{
+          range: { start: startIdx + 1, end: endIdx },
           text: withLineNumbers ? numberSourceLines(slice, startIdx + 1) : slice,
-          ranges: [{ start: startIdx + 1, end: endIdx }],
-        };
+        }];
       };
 
       /**
@@ -4507,10 +4721,7 @@ export class ToolHandler {
        * body is never cut, and the members are chosen by the same importance the
        * cluster ranking uses. Returns null when nothing needed shrinking.
        */
-      const shrinkCluster = (
-        c: ExploreCluster,
-        cap: number,
-      ): { text: string; ranges: ExploreLineRange[] } | null => {
+      const shrinkCluster = (c: ExploreCluster, cap: number): SectionPart[] | null => {
         if (c.members.length < 2) return null;
         const byImportance = [...c.members].sort((a, b) =>
           b.importance - a.importance || (a.end - a.start) - (b.end - b.start) || a.start - b.start);
@@ -4535,11 +4746,30 @@ export class ToolHandler {
           if (last && r.start <= last.end + gapThreshold) last.end = Math.max(last.end, r.end);
           else merged.push({ start: r.start, end: r.end });
         }
-        const sections = merged.map((m) => buildSection(m));
-        return {
-          text: sections.map((s) => s.text).join(GAP_MARKER),
-          ranges: sections.flatMap((s) => s.ranges),
-        };
+        return merged.flatMap((m) => buildSection(m));
+      };
+
+      /**
+       * One cluster's final parts: built, shrunk if it overruns `cap`, then
+       * passed through the session history (CG-18).
+       *
+       * The shrink decision reads the DEDUPED length on purpose. A cluster whose
+       * bytes the agent already holds costs this response nothing, so shrinking
+       * it on its raw size would drop new symbols to make room for source that
+       * is not being sent — spending the file's budget on nothing.
+       */
+      const renderCluster = (
+        c: ExploreCluster,
+        cap: number,
+      ): { parts: SectionPart[]; covered: ExploreLineRange[]; shrunk: boolean } => {
+        const base = dedupeSpans(buildSection(c));
+        if (sectionText(base.parts).length <= cap) {
+          return { parts: base.parts, covered: base.covered, shrunk: false };
+        }
+        const shrunk = shrinkCluster(c, cap);
+        if (shrunk === null) return { parts: base.parts, covered: base.covered, shrunk: false };
+        const dd = dedupeSpans(shrunk);
+        return { parts: dd.parts, covered: dd.covered, shrunk: true };
       };
 
       // Rank clusters for inclusion under the per-file cap. Entry-point
@@ -4586,23 +4816,28 @@ export class ToolHandler {
       // spine can't run away or starve co-flow files entirely.
       const SPINE_CEILING = Math.min(Math.round(allowance * 1.5), headroom);
       const chosenIndices = new Set<number>();
-      // Shrunk renders for oversize clusters, by cluster index (CG-12). Computed
+      // Final renders (deduped, shrunk where oversize) by cluster index. Computed
       // during selection and reused at emission so the two never disagree.
-      const shrunkSections = new Map<number, { text: string; ranges: ExploreLineRange[] }>();
+      const renderedClusters = new Map<number, ReturnType<typeof renderCluster>>();
+      let anyClusterShrunk = false;
       let projectedChars = 0;
       for (const rc of rankedClusters) {
-        const sectionLen = buildSection(rc.c).text.length + (chosenIndices.size > 0 ? GAP_MARKER.length : 0);
         // The top-ranked cluster is always taken — an empty file section sends the
         // agent to Read, negating the savings. But "always taken" is not "taken at
         // any size": when it overruns the reservation it is SHRUNK to the
         // highest-importance whole symbol ranges inside it, so a single-cluster
-        // god-file spends its allotment instead of the whole response's.
-        if (chosenIndices.size === 0) {
-          const cap = rc.c.hasSpine ? SPINE_CEILING : fileBudget;
-          const shrunk = sectionLen > cap ? shrinkCluster(rc.c, cap) : null;
-          if (shrunk !== null) shrunkSections.set(rc.idx, shrunk);
+        // god-file spends its allotment instead of the whole response's. Later
+        // clusters are never shrunk — they either fit or wait for another call.
+        const first = chosenIndices.size === 0;
+        const cap = rc.c.hasSpine ? SPINE_CEILING : fileBudget;
+        const section = renderCluster(rc.c, first ? cap : Infinity);
+        const text = sectionText(section.parts);
+        const sectionLen = text.length + (!first && text.length > 0 ? GAP_MARKER.length : 0);
+        if (first) {
+          renderedClusters.set(rc.idx, section);
+          anyClusterShrunk = anyClusterShrunk || section.shrunk;
           chosenIndices.add(rc.idx);
-          projectedChars += shrunk !== null ? shrunk.text.length : sectionLen;
+          projectedChars += sectionLen;
           continue;
         }
         // A spine cluster (the rendered call path) is the flow answer — include it
@@ -4611,6 +4846,7 @@ export class ToolHandler {
         const fits = projectedChars + sectionLen <= fileBudget;
         const spineFits = rc.c.hasSpine && projectedChars + sectionLen <= SPINE_CEILING;
         if (!fits && !spineFits) continue;
+        renderedClusters.set(rc.idx, section);
         chosenIndices.add(rc.idx);
         projectedChars += sectionLen;
       }
@@ -4619,13 +4855,18 @@ export class ToolHandler {
       let fileSection = '';
       const allSymbols: string[] = [];
       const sectionRanges: ExploreLineRange[] = [];
+      const coveredRanges: ExploreLineRange[] = [];
       for (let i = 0; i < clusters.length; i++) {
         if (!chosenIndices.has(i)) continue;
         const cluster = clusters[i]!;
-        const section = shrunkSections.get(i) ?? buildSection(cluster);
-        if (fileSection.length > 0) fileSection += GAP_MARKER;
-        fileSection += section.text;
-        sectionRanges.push(...section.ranges);
+        const section = renderedClusters.get(i)!;
+        const text = sectionText(section.parts);
+        if (text.length > 0) {
+          if (fileSection.length > 0) fileSection += GAP_MARKER;
+          fileSection += text;
+        }
+        sectionRanges.push(...section.parts.map((p) => p.range));
+        coveredRanges.push(...section.covered);
         allSymbols.push(...cluster.symbols);
       }
 
@@ -4635,7 +4876,7 @@ export class ToolHandler {
       // method is useless (the agent just Reads the rest for the other half), which
       // is the very fallback explore exists to prevent. A pathological file is
       // bounded by the cluster SELECTION above + the total hard ceiling.
-      if (chosenIndices.size < clusters.length || shrunkSections.size > 0) {
+      if (chosenIndices.size < clusters.length || anyClusterShrunk) {
         anyFileTrimmed = true;
       }
 
@@ -4673,19 +4914,62 @@ export class ToolHandler {
         continue;
       }
 
-      lines.push(fileHeader);
-      lines.push('');
-      lines.push('```' + lang);
-      lines.push(fileSection);
-      lines.push('```');
-      lines.push('');
+      // The undeduped render of the same clusters, needed only if this file ends
+      // up fully back-referenced AND the whole call finds nothing new to say —
+      // see `suppressedFallback`. Built lazily: on every other call it is dead
+      // weight.
+      const fullClusterParts = fileSection.length === 0
+        ? clusters.flatMap((c, i) => (chosenIndices.has(i) ? buildSection(c) : []))
+        : [];
+      emitFileSection({
+        header: fileHeader,
+        body: fileSection,
+        ranges: sectionRanges,
+        covered: mergeRanges(coveredRanges),
+        overhead: 200,
+        mode: 'clusters',
+        clipped: chosenIndices.size < clusters.length,
+        fullBody: sectionText(fullClusterParts),
+        fullRanges: fullClusterParts.map((p) => p.range),
+      });
+    }
+
+    // Anti-abandonment restore (CG-18). Dedup withheld everything and nothing new
+    // took its place — the response would be pointers only, which is the shape
+    // that reads as "codegraph found nothing" and sends the agent to Read for
+    // good. Put the top suppressed file back, in full, and keep its pointer off.
+    // Deliberately checked against `newSourceChars` (source THIS call emitted)
+    // rather than the response length: the flow and blast-radius sections are
+    // always there, and they are not what makes a response feel sufficient.
+    // Cast, not annotation: the only writer is the render loop's `emitFileSection`
+    // closure, which TypeScript's flow analysis cannot see, so it narrows the
+    // variable to `null` here and the truthiness check below would be `never`.
+    const restore = suppressedFallback as SuppressedFallback | null;
+    if (newSourceChars === 0 && restore) {
+      if (totalChars + restore.sourceChars + restore.overhead <= renderCeiling) {
+        lines.splice(restore.at, restore.replacing, ...restore.section);
+        totalChars += restore.sourceChars + restore.overhead;
+        sourceSpent += restore.sourceChars;
+        newSourceChars += restore.sourceChars;
+        filesIncluded++;
+        const idx = backReferencedFiles.indexOf(restore.filePath);
+        if (idx >= 0) backReferencedFiles.splice(idx, 1);
+        emittedByFile.set(restore.filePath, {
+          ranges: [...restore.ranges],
+          bytes: restore.sourceChars,
+          fingerprint: restore.fingerprint,
+        });
+        diag?.recordRender(restore.filePath, 'clusters', restore.sourceChars, false);
+        diag?.recordDedup(restore.filePath, 0, []);
+      }
+    }
 
-      totalChars += fileSection.length + 200;
-      sourceSpent += fileSection.length;
-      diag?.recordRender(filePath, 'clusters', fileSection.length, chosenIndices.size < clusters.length);
-      noteEmitted(filePath, sectionRanges, fileSection.length);
-      renderedFilePaths.push(filePath);
-      filesIncluded++;
+    // The back-reference convention, stated once where the verbatim guarantee is
+    // (#1474 does the same for drift). Without it a pointer reads as an
+    // apology for missing source rather than as an index into source the agent
+    // already has.
+    if (backReferencedFiles.length > 0) {
+      lines[verbatimHeaderIdx] += ` (Files marked **"Already sent earlier in this conversation"** are not repeated: their source came back on an earlier codegraph_explore call in THIS conversation and the file has not changed since, so that copy is exact and current — scroll back for it rather than re-fetching or Reading.)`;
     }
 
     // Drift epilogue (#1474). The "verbatim / do not Read" guarantee above
@@ -4833,12 +5117,22 @@ export class ToolHandler {
     // Session record (CG-17): only the files that SURVIVED the hard ceiling —
     // a section the truncation dropped was never delivered, and recording it
     // would let a later call withhold source the agent has never seen.
+    //
+    // A back-referenced file records its spans at ZERO bytes (CG-18) — it is
+    // still source the agent holds for this file, which is what the record
+    // means; dropping it would let the span age out of the retained window and
+    // be re-served for nothing.
     const emittedFiles: ExploreFileEmission[] = [];
     let sourceBytes = 0;
     for (const fp of survivors) {
       const emitted = emittedByFile.get(fp);
-      if (!emitted || emitted.bytes <= 0) continue;
-      emittedFiles.push({ path: fp, ranges: emitted.ranges, bytes: emitted.bytes });
+      if (!emitted || emitted.ranges.length === 0) continue;
+      emittedFiles.push({
+        path: fp,
+        ranges: emitted.ranges,
+        bytes: emitted.bytes,
+        fingerprint: emitted.fingerprint,
+      });
       sourceBytes += emitted.bytes;
     }
     return this.exploreResult(finalText, {