diff --git a/experiments/atomic-codemode/README.md b/experiments/atomic-codemode/README.md
index 5b223477cb..7c27cc1400 100644
--- a/experiments/atomic-codemode/README.md
+++ b/experiments/atomic-codemode/README.md
@@ -214,3 +214,12 @@ The trace reveals two format sources at each shared call, verified against byte
 and machine evidence. [Costs and source review](trials.md) also record a direct
 documentation-lookup miss; named discovery needs fixing before rerunning the
 same task. No general adapter speedup follows from that first pair.
+
+Named reference lookup now accepts canonical IDs or exact displayed names,
+including space/comma-separated lists. One presentation map supplies direct
+registration and documentation names; unmatched terms remain explicit. Selected
+schemas come from named contracts, use input semantics (defaulted fields stay
+optional), and are cached immutably by Zod schema identity for the process.
+Validation stays in the API registry; documentation has its own module. Both
+actual MCP catalogs and all fourteen reference schemas validate. The unchanged
+PHI question/oracle will be rerun after this discovery correction.
diff --git a/experiments/atomic-codemode/api.mjs b/experiments/atomic-codemode/api.mjs
index f5558fd64f..5053981fc0 100644
--- a/experiments/atomic-codemode/api.mjs
+++ b/experiments/atomic-codemode/api.mjs
@@ -3,6 +3,7 @@ import { z } from "zod";
 import { KunaFactOwner } from "./provider.mjs";
 import { FactFailure } from "./fact-error.mjs";
 import { MAX_BYTE_BATCH_BYTES } from "./limits.mjs";
+import { createReference } from "./reference.mjs";
 
 const hex = z.string().regex(/^0x(?:0|[1-9a-f][0-9a-f]{0,15})$/u);
 const snapshot = z.string().startsWith("snap_");
@@ -250,36 +251,6 @@ export const methods = {
   ),
 };
 
-// Compact return contracts let code compose before first observing a response.
-const returns = {
-  bytes:
-    "data:{results:[{ok,address,source:{evidence_id,sha256},hex,returned_bytes,end_address,coverage:{status,requested_bytes,provider_truncated,notes,original_file_mapping,runtime_memory}}|{ok:false,address,error}]}; ranges are [address,end_address). Completeness concerns requested bytes, not the provider truncation flag or adjacent bytes. Complete native hexdump and metadata remain in Evidence.",
-  functions:
-    "data:{source:{evidence_id,sha256},items:[{address,name,aliases,size}],total,next_offset,coverage}; size is an upper bound, or zero if unmeasured. Multiple matching addresses are retained, never selected by catalog order or display name alone.",
-  instructions:
-    "data:{results:[{ok,address,source:{evidence_id,sha256},items:[{address,size,status,bytes?,text?,mnemonic?,operands?}],resume_address,coverage}|{ok:false,address,error}]}; decoded rows describe selected machine bytes, not optimized IR branches. Partial batches retain successful windows.",
-  strings:
-    "data:{source:{evidence_id,sha256},items:[{address,value,string:{encoding,byte_length}}],total,next_offset,coverage}",
-  references:
-    "data:{results:[{ok,address,source:{evidence_id},items:[{source_row,from,to,kind,fromFunction:{address,name}|null,toFunction:{address,name}|null,instruction}],total,next_offset,coverage}|{ok:false,address,error}]}. source_row is the zero-based row in retained native xrefs; Evidence identity plus source_row identifies an occurrence. Coverage preserves examined/excluded/unattributed counts and unknown function scope/discovery. fields projects optional columns; endpoints/kind/source_row stay.",
-  snapshot:
-    "data:{snapshot:string,entry,source:{evidence_id,sha256},facets:{code:{availability},recovered_ir:{availability,error?},operations:{availability,scope?,count?,root_count?,definition_frontier_count?,error?},calls:{availability,count?,by_opcode?:[{opcode,known_target_count,unknown_target_count}],coverage?,error?},values:{availability,scope?,count?,error?}},coverage}. Call counts cover all retained recovered calls, including is_dead rows, not complete machine/runtime calls; target knowledge comes from a non-null native target, independent of opcode. An unavailable facet omits counts; an available empty call facet reports zeros. The complete graph can be unavailable while operations reports a bounded projection count; an unavailable operation facet has unknown/null counts, never a fabricated empty set; code remains readable through the same handle.",
-  operations:
-    "data:{items:[{id,origin_address,block,source_line,kind,statement,definitions,constants,inputs?,output?,opcode?,is_dead?}],total,next_offset,evidence_id,coverage}. Native inputs:[{input_index,value_id,phi_predecessor,phi_predecessor_edge}], output:value_id|null; native constants include value_id/input_index and exact u64 value offset with printed_size_bytes (native width), not arbitrary-width computed values; definitions:[{definition,use,input_index,value_id,phi_predecessor,phi_predecessor_edge}]. Diagnostic definitions use printed occurrence instead. fields projects columns; identity and native is_dead remain. A call-rooted projection reports retained facts only, with unknown CFG and explicit definition frontier coverage.",
-  relations:
-    "data:{items:definition/use edges OR CFG edges{from,to,operation,polarity?,condition_value?,condition_test?} OR controllers{controller,dependent,edge},total,next_offset,evidence_id,coverage,relation_coverage?,unretained_seeds?}. definitions/uses seeds are operation-ID strings; incoming/outgoing/controllers seeds are numeric block IDs. Native def/use edges include input_index,value_id,phi_predecessor; diagnostic edges include occurrence only.",
-  values:
-    "data:{items:[{id,space,offset,size_bytes,is_constant,is_input,is_annotation,definition,type_name}],total,next_offset,evidence_id,coverage}; definitions are operation IDs, offsets are exact hex strings. When the graph is unavailable, values may come from a bounded definition projection or only the call boundary; coverage states that scope and operations/definitions may be unreadable.",
-  calls:
-    "data:{items:[{id,origin_address,block,opcode,spec_available,is_dead,target:{space,offset}|null,target_name,arguments:[{input_index,value_id,storage:{space,offset,size_bytes}|null,storage_authority}],output}],total,next_offset,missing,evidence_id,coverage}. fields selects target/target_name/arguments/output/prototype/stack_offset/target_value_id/is_dead. Values may come from a bounded call-rooted definition projection or call-boundary set when the graph is unavailable; coverage states that scope. Calls include all retained call operations; null facts are unknown, not proof of no arguments or runtime binding. Candidate cross-function links require matching target identity and exact passing/input storage; join/subregister/alias interpretation remains unknown.",
-  blocks:
-    "data:{items:[{id,origin_start,operations,predecessors,successors:[{target,index,polarity,condition_value,condition_test}]}],total,next_offset,evidence_id,coverage}; IDs are local to this snapshot.",
-  slice:
-    "data:{operations:[operation rows as above],coverage:{status,boundaries:[{id,reason}],missing,missing_reasons?,source_scope?,source_issues,runtime_reachability,memory_alias_dependencies},value_frontier?:[{value_id?|operation?,input_index?,reason}],evidence_id}",
-  code: "data:{evidence_id,start_line,language:string|null,text,total_lines,next_offset,coverage}; language is native-reported or unknown. Read/filter full reconstructed text within Code Mode without returning it all.",
-  evidence:
-    "data:{source:{evidence_id,sha256,bytes,arguments},text,total_code_units,next_offset}; source has complete native output, including code before the SSA graph.",
-};
 methods.bytes.input = methods.bytes.input.superRefine((value, context) => {
   // Pattern failures need not prevent object refinements from running in Zod.
   // Only the named window contract may admit values to exact u64 arithmetic.
@@ -426,32 +397,4 @@ export class AtomicSession {
   }
 }
 
-export const reference = (query = "") => {
-  const keys = Object.keys(methods).filter(
-    (key) =>
-      query === "" ||
-      key.includes(query) ||
-      methods[key].description.toLowerCase().includes(query.toLowerCase()),
-  );
-  return {
-    language:
-      "JavaScript async function body; return a JSON value. All rea methods return {ok,context,data} or {ok:false,error}.",
-    methods: keys.map((name) => ({
-      name: `rea.${name}`,
-      description: methods[name].description,
-      input_schema: z.toJSONSchema(methods[name].input),
-      returns: returns[name],
-      example: methods[name].example,
-    })),
-    limits: {
-      execution_heap_mib: 64,
-      max_host_calls: 64,
-      output_utf8_bytes: 32768,
-    },
-    notes: [
-      "No process, filesystem, network, imports or Node globals in the execution environment.",
-      "Select facts inside code, return only what the question needs, and keep real source IDs and unknowns.",
-      "A fresh JavaScript environment is used per execute_javascript call; analysis snapshots live until close_binary.",
-    ],
-  };
-};
+export const reference = createReference(methods);
diff --git a/experiments/atomic-codemode/native-engine.md b/experiments/atomic-codemode/native-engine.md
index 1a2f380e63..3a2a99d08e 100644
--- a/experiments/atomic-codemode/native-engine.md
+++ b/experiments/atomic-codemode/native-engine.md
@@ -542,3 +542,33 @@ stages and workspace gates remain unexecuted; the patch is not upstream-ready.
 No whole-repository typecheck pass is claimed beyond the previously recorded
 resource limitation. The [PHI-format task/oracle](projection-oracle.md) are fixed
 before real-model launches. No model benefit is assumed from these smaller facts.
+
+## Named reference discovery and input schemas
+
+The first PHI model pair completes correctly but exposes a documentation boundary:
+direct help displays `facts_*` names while lookup only recognizes raw method
+substrings. A multi-name query returns no matches and causes a full-reference
+fallback. Registration and help now share one explicit name map, with canonical
+identity separate from presentation. Exact lists preserve caller order,
+deduplicate names and retain unmatched terms. Topic/all-contract lookup remain;
+ambiguous labels fail instead of choosing by catalog position.
+
+The real client verifier also catches that plain `z.toJSONSchema` defaults to
+output semantics, making defaulted `offset`/`limit` falsely required in advertised
+input schemas. Reference generation now explicitly selects `io:input`. Converted
+schemas are frozen and weakly cached by schema identity; a replacement schema
+invalidates the conversion, while description/presentation is read separately.
+The documentation module removes the adapter rename pass. No target analysis,
+live-result caching or native-engine change is involved.
+
+The shared suite passes 55 tests. `verify-discovery.mjs` checks both real SDK
+catalogs and reference responses without opening a target, compiles every catalog
+and all fourteen reference schemas with Ajv2020, and validates the same
+omitted-default requests against named reference/direct contracts. It proves the
+six-name query matches all requested contracts without a miss. The corrected
+verifier takes 1.628 family wall / 1.449 CPU seconds, 128.9 MiB kernel peak,
+cleanup verified and OOM 0. Its original 1.730 / 1.487 seconds, 128.1 MiB failed
+omitted-default check remains recorded. Six contracts occupy 10,835 Code Mode /
+10,360 direct bytes, versus 21,746 / 20,699 for all fourteen. Bytes do not prove
+token or time savings. The same PHI question/oracle are retained for the next
+actual model pair.
diff --git a/experiments/atomic-codemode/reference.mjs b/experiments/atomic-codemode/reference.mjs
new file mode 100644
index 0000000000..a8c1a0697f
--- /dev/null
+++ b/experiments/atomic-codemode/reference.mjs
@@ -0,0 +1,125 @@
+// Named documentation selection; adapters supply their exact registered labels.
+import { z } from "zod";
+import { FactFailure } from "./fact-error.mjs";
+import { freezeFacts } from "./fact-reads.mjs";
+
+// Compact return contracts let code compose before first observing a response.
+const returns = {
+  bytes:
+    "data:{results:[{ok,address,source:{evidence_id,sha256},hex,returned_bytes,end_address,coverage:{status,requested_bytes,provider_truncated,notes,original_file_mapping,runtime_memory}}|{ok:false,address,error}]}; ranges are [address,end_address). Completeness concerns requested bytes, not the provider truncation flag or adjacent bytes. Complete native hexdump and metadata remain in Evidence.",
+  functions:
+    "data:{source:{evidence_id,sha256},items:[{address,name,aliases,size}],total,next_offset,coverage}; size is an upper bound, or zero if unmeasured. Multiple matching addresses are retained, never selected by catalog order or display name alone.",
+  instructions:
+    "data:{results:[{ok,address,source:{evidence_id,sha256},items:[{address,size,status,bytes?,text?,mnemonic?,operands?}],resume_address,coverage}|{ok:false,address,error}]}; decoded rows describe selected machine bytes, not optimized IR branches. Partial batches retain successful windows.",
+  strings:
+    "data:{source:{evidence_id,sha256},items:[{address,value,string:{encoding,byte_length}}],total,next_offset,coverage}",
+  references:
+    "data:{results:[{ok,address,source:{evidence_id},items:[{source_row,from,to,kind,fromFunction:{address,name}|null,toFunction:{address,name}|null,instruction}],total,next_offset,coverage}|{ok:false,address,error}]}. source_row is the zero-based row in retained native xrefs; Evidence identity plus source_row identifies an occurrence. Coverage preserves examined/excluded/unattributed counts and unknown function scope/discovery. fields projects optional columns; endpoints/kind/source_row stay.",
+  snapshot:
+    "data:{snapshot:string,entry,source:{evidence_id,sha256},facets:{code:{availability},recovered_ir:{availability,error?},operations:{availability,scope?,count?,root_count?,definition_frontier_count?,error?},calls:{availability,count?,by_opcode?:[{opcode,known_target_count,unknown_target_count}],coverage?,error?},values:{availability,scope?,count?,error?}},coverage}. Call counts cover all retained recovered calls, including is_dead rows, not complete machine/runtime calls; target knowledge comes from a non-null native target, independent of opcode. An unavailable facet omits counts; an available empty call facet reports zeros. The complete graph can be unavailable while operations reports a bounded projection count; an unavailable operation facet has unknown/null counts, never a fabricated empty set; code remains readable through the same handle.",
+  operations:
+    "data:{items:[{id,origin_address,block,source_line,kind,statement,definitions,constants,inputs?,output?,opcode?,is_dead?}],total,next_offset,evidence_id,coverage}. Native inputs:[{input_index,value_id,phi_predecessor,phi_predecessor_edge}], output:value_id|null; native constants include value_id/input_index and exact u64 value offset with printed_size_bytes (native width), not arbitrary-width computed values; definitions:[{definition,use,input_index,value_id,phi_predecessor,phi_predecessor_edge}]. Diagnostic definitions use printed occurrence instead. fields projects columns; identity and native is_dead remain. A call-rooted projection reports retained facts only, with unknown CFG and explicit definition frontier coverage.",
+  relations:
+    "data:{items:definition/use edges OR CFG edges{from,to,operation,polarity?,condition_value?,condition_test?} OR controllers{controller,dependent,edge},total,next_offset,evidence_id,coverage,relation_coverage?,unretained_seeds?}. definitions/uses seeds are operation-ID strings; incoming/outgoing/controllers seeds are numeric block IDs. Native def/use edges include input_index,value_id,phi_predecessor; diagnostic edges include occurrence only.",
+  values:
+    "data:{items:[{id,space,offset,size_bytes,is_constant,is_input,is_annotation,definition,type_name}],total,next_offset,evidence_id,coverage}; definitions are operation IDs, offsets are exact hex strings. When the graph is unavailable, values may come from a bounded definition projection or only the call boundary; coverage states that scope and operations/definitions may be unreadable.",
+  calls:
+    "data:{items:[{id,origin_address,block,opcode,spec_available,is_dead,target:{space,offset}|null,target_name,arguments:[{input_index,value_id,storage:{space,offset,size_bytes}|null,storage_authority}],output}],total,next_offset,missing,evidence_id,coverage}. fields selects target/target_name/arguments/output/prototype/stack_offset/target_value_id/is_dead. Values may come from a bounded call-rooted definition projection or call-boundary set when the graph is unavailable; coverage states that scope. Calls include all retained call operations; null facts are unknown, not proof of no arguments or runtime binding. Candidate cross-function links require matching target identity and exact passing/input storage; join/subregister/alias interpretation remains unknown.",
+  blocks:
+    "data:{items:[{id,origin_start,operations,predecessors,successors:[{target,index,polarity,condition_value,condition_test}]}],total,next_offset,evidence_id,coverage}; IDs are local to this snapshot.",
+  slice:
+    "data:{operations:[operation rows as above],coverage:{status,boundaries:[{id,reason}],missing,missing_reasons?,source_scope?,source_issues,runtime_reachability,memory_alias_dependencies},value_frontier?:[{value_id?|operation?,input_index?,reason}],evidence_id}",
+  code: "data:{evidence_id,start_line,language:string|null,text,total_lines,next_offset,coverage}; language is native-reported or unknown. Read/filter full reconstructed text within Code Mode without returning it all.",
+  evidence:
+    "data:{source:{evidence_id,sha256,bytes,arguments},text,total_code_units,next_offset}; source has complete native output, including code before the SSA graph.",
+};
+const referenceSchemas = new WeakMap();
+const schemaFor = (input) => {
+  if (!referenceSchemas.has(input))
+    referenceSchemas.set(
+      input,
+      freezeFacts(z.toJSONSchema(input, { io: "input" })),
+    );
+  return referenceSchemas.get(input);
+};
+function referenceNames(methods, names) {
+  const keys = Object.keys(methods),
+    lookup = new Map(keys.map((key) => [key, key])),
+    labels = {};
+  if (Object.keys(names).some((key) => !Object.hasOwn(methods, key)))
+    throw new FactFailure(
+      "invalid_input",
+      "Unknown method in reference presentation",
+    );
+  for (const key of keys) {
+    const label = names[key] ?? `rea.${key}`;
+    if (
+      typeof label !== "string" ||
+      !label ||
+      (lookup.has(label) && lookup.get(label) !== key)
+    )
+      throw new FactFailure(
+        "invalid_input",
+        "Ambiguous or invalid reference method name",
+      );
+    lookup.set(label, key);
+    labels[key] = label;
+  }
+  return { lookup, labels };
+}
+function selectReference(methods, query, lookup) {
+  const normalized = query.trim();
+  if (!normalized)
+    return { keys: Object.keys(methods), selection: "all", unmatched: [] };
+  const terms = normalized.split(/[\s,]+/u),
+    named = terms.map((term) => lookup.get(term));
+  if (named.some(Boolean))
+    return {
+      keys: [...new Set(named.filter(Boolean))],
+      selection: "named",
+      unmatched: terms.filter((term) => !lookup.has(term)),
+    };
+  const topic = normalized.toLowerCase();
+  const keys = Object.keys(methods).filter(
+    (key) =>
+      key.includes(topic) ||
+      methods[key].description.toLowerCase().includes(topic),
+  );
+  return { keys, selection: "topic", unmatched: keys.length ? [] : [query] };
+}
+export const createReference =
+  (methods) =>
+  (query = "", { names = {}, language, includeExamples = true } = {}) => {
+    const { lookup, labels } = referenceNames(methods, names),
+      selected = selectReference(methods, query, lookup);
+    return {
+      language:
+        language ??
+        "JavaScript async function body; return a JSON value. All rea methods return {ok,context,data} or {ok:false,error}.",
+      methods: selected.keys.map((method) => ({
+        method,
+        name: labels[method],
+        description: methods[method].description,
+        input_schema: schemaFor(methods[method].input),
+        returns: returns[method],
+        ...(includeExamples ? { example: methods[method].example } : {}),
+      })),
+      coverage: {
+        declared_methods: Object.keys(methods).length,
+        matched_methods: selected.keys.length,
+        selection: selected.selection,
+      },
+      unmatched_queries: selected.unmatched,
+      limits: {
+        execution_heap_mib: 64,
+        max_host_calls: 64,
+        output_utf8_bytes: 32768,
+      },
+      notes: [
+        "Select exact displayed method names or canonical method IDs, separated by spaces/commas; a topic query searches descriptions. Empty query returns all contracts.",
+        "No process, filesystem, network, imports or Node globals in the execution environment.",
+        "Select facts inside code, return only what the question needs, and keep real source IDs and unknowns.",
+        "A fresh JavaScript environment is used per execute_javascript call; analysis snapshots live until close_binary.",
+      ],
+    };
+  };
diff --git a/experiments/atomic-codemode/reference.test.mjs b/experiments/atomic-codemode/reference.test.mjs
new file mode 100644
index 0000000000..1095733d00
--- /dev/null
+++ b/experiments/atomic-codemode/reference.test.mjs
@@ -0,0 +1,71 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+import Ajv2020 from "ajv/dist/2020.js";
+import { methods, reference } from "./api.mjs";
+
+test("named reference lists preserve caller order and exact schemas across presentations", () => {
+  const names = Object.fromEntries(
+    Object.keys(methods).map((name) => [name, `facts_${name}`]),
+  );
+  const result = reference(
+    "facts_values, facts_snapshot facts_values unknown",
+    { names, includeExamples: false },
+  );
+  assert.deepEqual(
+    result.methods.map((m) => m.method),
+    ["values", "snapshot"],
+  );
+  assert.deepEqual(
+    result.methods.map((m) => m.name),
+    ["facts_values", "facts_snapshot"],
+  );
+  assert.deepEqual(result.unmatched_queries, ["unknown"]);
+  assert.equal(result.coverage.declared_methods, 14);
+  assert.equal(result.coverage.matched_methods, 2);
+  assert.equal(result.coverage.selection, "named");
+  const javascript = reference("rea.values snapshot");
+  assert.deepEqual(
+    javascript.methods.map((m) => m.method),
+    ["values", "snapshot"],
+  );
+  assert.deepEqual(
+    result.methods.map((m) => m.input_schema),
+    javascript.methods.map((m) => m.input_schema),
+  );
+  const validate = new Ajv2020({ strict: false }).compile(
+    result.methods[1].input_schema,
+  );
+  assert.equal(validate({ entry: "0xea6d0" }), true);
+  assert.equal(validate({ snapshot: "wrong contract" }), false);
+  const validateValues = new Ajv2020({ strict: false }).compile(
+    result.methods[0].input_schema,
+  );
+  assert.equal(validateValues({ snapshot: "snap_example", ids: ["v1"] }), true);
+  assert.equal(
+    methods.values.input.parse({ snapshot: "snap_example" }).limit,
+    20,
+  );
+  assert.equal(Object.hasOwn(result.methods[0], "example"), false);
+});
+
+test("topic/all reference selection and shared schema ownership remain explicit", () => {
+  assert.equal(reference().methods.length, 14);
+  assert.equal(reference("no-such-topic").coverage.matched_methods, 0);
+  assert.ok(
+    reference("memory aliases").methods.some((m) => m.method === "slice"),
+  );
+  const before = reference("snapshot").methods[0];
+  assert.throws(() => {
+    before.input_schema.properties.entry.type = "number";
+  }, TypeError);
+  const after = reference("snapshot").methods[0];
+  assert.equal(after.input_schema.properties.entry.type, "string");
+  assert.throws(
+    () => reference("values", { names: { snapshot: "values" } }),
+    /Ambiguous/,
+  );
+  assert.throws(
+    () => reference("values", { names: { unknown: "facts_values" } }),
+    /Unknown/,
+  );
+});
diff --git a/experiments/atomic-codemode/server.mjs b/experiments/atomic-codemode/server.mjs
index 5c2e451266..7194cadecf 100644
--- a/experiments/atomic-codemode/server.mjs
+++ b/experiments/atomic-codemode/server.mjs
@@ -7,9 +7,18 @@ import { executeJavaScript } from "./executor.mjs";
 import { TARGET_CONTENT_RESULT_META } from "../../dist/server/toolResultEncoding.js";
 import { appendFile } from "node:fs/promises";
 
+const DIRECT_REFERENCE_LANGUAGE =
+  "Direct MCP calls: use the displayed facts_* tools with the same JSON arguments; results have {ok,context,data}.";
 const session = new AtomicSession();
 const createServer = () => {
   const server = new McpServer({ name: "rea-codemode", version: "0.1.0" });
+  const direct = process.env.REA_ATOMIC_ADAPTER === "direct";
+  const apiNames = Object.fromEntries(
+    Object.keys(methods).map((name) => [
+      name,
+      direct ? `facts_${name}` : `rea.${name}`,
+    ]),
+  );
   const encode = (value) => ({
     content: [{ type: "text", text: JSON.stringify(value) }],
     _meta: TARGET_CONTENT_RESULT_META,
@@ -64,26 +73,19 @@ const createServer = () => {
   );
   register(
     "reference",
-    "Look up the rea JavaScript API by method name or analyst concept before writing Code Mode calls. Empty query returns the complete API reference.",
+    "Look up analysis contracts by exact displayed method names or canonical method IDs, separated by spaces or commas, or search one analyst concept. Request only needed methods; empty query returns all contracts.",
     z.strictObject({ query: z.string().default("") }),
-    (input) => {
-      const docs = reference(input.query);
-      if (process.env.REA_ATOMIC_ADAPTER === "direct") {
-        docs.language =
-          "Direct MCP calls: use facts_<method> with the same JSON arguments; results have {ok,context,data}.";
-        docs.methods = docs.methods.map((method) => ({
-          ...method,
-          name: method.name.replace("rea.", "facts_"),
-          example: undefined,
-        }));
-      }
-      return docs;
-    },
+    (input) =>
+      reference(input.query, {
+        names: apiNames,
+        includeExamples: !direct,
+        language: direct ? DIRECT_REFERENCE_LANGUAGE : undefined,
+      }),
   );
-  if (process.env.REA_ATOMIC_ADAPTER === "direct") {
+  if (direct) {
     for (const [name, contract] of Object.entries(methods))
       register(
-        `facts_${name}`,
+        apiNames[name],
         contract.description,
         contract.input,
         (input, signal) => session.call(name, input, signal),
diff --git a/experiments/atomic-codemode/verify-discovery.mjs b/experiments/atomic-codemode/verify-discovery.mjs
new file mode 100644
index 0000000000..778a0a530e
--- /dev/null
+++ b/experiments/atomic-codemode/verify-discovery.mjs
@@ -0,0 +1,118 @@
+// Verify actual SDK-converted catalogs and named help without target analysis.
+import assert from "node:assert/strict";
+import { writeFile } from "node:fs/promises";
+import { resolve } from "node:path";
+import { Client } from "@modelcontextprotocol/client";
+import { StdioClientTransport } from "@modelcontextprotocol/client/stdio";
+import Ajv2020 from "ajv/dist/2020.js";
+import {
+  createVerifierRun,
+  completeVerifierRun,
+  assertVerifierCleanupComplete,
+} from "../../scripts/lib/verifier-run.mjs";
+
+const [output] = process.argv.slice(2);
+const run = createVerifierRun(),
+  results = [],
+  failures = [];
+for (const direct of [false, true]) {
+  const client = new Client({
+    name: "rea-discovery-verifier",
+    version: "0.1.0",
+  });
+  const transport = new StdioClientTransport({
+    command: process.execPath,
+    args: [resolve("experiments/atomic-codemode/server.mjs")],
+    env: { ...process.env, REA_ATOMIC_ADAPTER: direct ? "direct" : "codemode" },
+    stderr: "pipe",
+  });
+  const call = async (query) => {
+    const reply = await client.callTool({
+      name: "reference",
+      arguments: { query },
+    });
+    return JSON.parse(reply.content[0].text);
+  };
+  try {
+    await client.connect(transport);
+    const catalog = await client.listTools();
+    const prefix = direct ? "facts_" : "rea.";
+    const ids = [
+      "snapshot",
+      "operations",
+      "relations",
+      "values",
+      "instructions",
+      "bytes",
+    ];
+    const selected = await call(ids.map((name) => prefix + name).join(" "));
+    assert.deepEqual(
+      selected.methods.map((m) => m.method),
+      ids,
+    );
+    assert.deepEqual(selected.unmatched_queries, []);
+    assert.equal(selected.coverage.declared_methods, 14);
+    const ajv = new Ajv2020({ strict: false });
+    for (const tool of catalog.tools) ajv.compile(tool.inputSchema);
+    for (const method of selected.methods) {
+      ajv.compile(method.input_schema);
+      assert.equal(method.name, prefix + method.method);
+      if (direct)
+        assert.ok(catalog.tools.some((tool) => tool.name === method.name));
+    }
+    for (const [name, good, bad] of [
+      ["snapshot", { entry: "0xea6d0" }, { snapshot: "snap_other" }],
+      ["values", { snapshot: "snap_other", ids: ["v1"] }, { entry: "0xea6d0" }],
+    ]) {
+      const method = selected.methods.find((m) => m.method === name);
+      const validators = [ajv.compile(method.input_schema)];
+      if (direct)
+        validators.push(
+          ajv.compile(
+            catalog.tools.find((t) => t.name === method.name).inputSchema,
+          ),
+        );
+      for (const validate of validators) {
+        assert.equal(validate(good), true);
+        assert.equal(validate(bad), false);
+      }
+    }
+    const missing = await call(`${prefix}values unknown`);
+    assert.deepEqual(
+      missing.methods.map((m) => m.method),
+      ["values"],
+    );
+    assert.deepEqual(missing.unmatched_queries, ["unknown"]);
+    const all = await call("");
+    assert.equal(all.methods.length, 14);
+    for (const method of all.methods) ajv.compile(method.input_schema);
+    assert.ok(JSON.stringify(selected).length < JSON.stringify(all).length);
+    results.push({
+      direct,
+      selected,
+      all_reference_bytes: Buffer.byteLength(JSON.stringify(all)),
+      selected_reference_bytes: Buffer.byteLength(JSON.stringify(selected)),
+      actual_catalog_and_named_schema_checks_passed: true,
+    });
+  } catch (error) {
+    failures.push(error.stack ?? String(error));
+  } finally {
+    await client.close();
+    await transport.close();
+  }
+}
+const lifecycle = await completeVerifierRun(run);
+assertVerifierCleanupComplete(lifecycle.process_lineage);
+await writeFile(
+  output,
+  JSON.stringify({
+    results,
+    failures,
+    lifecycle,
+    scope:
+      "Static contract/catalog checks; no native target analysis or model cost measurement",
+  }),
+  { flag: "wx" },
+);
+console.log(JSON.stringify({ output, lanes: results.length, failures }));
+if (failures.length) process.exitCode = 1;