diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e26e3970c..548e1c9f3c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -100,6 +100,8 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
+- **A documentation link to a file that is not there no longer gets its own graph node.** A Markdown link or path mention whose target basename no indexed file has minted an import node and a `contains` edge, even though the resolver's file-path arm could not match it. On supabase a full index now skips 10,394 of 14,038 Markdown import nodes and their `contains` edges. The reference is always kept, so the resolver's route, module and table arms still match one (a relative `api/users.json` link included), `codegraph sync` can resolve a target added later from the parked failed reference, and a skipped target stays in a separate `links:` part of the file digest so it remains searchable past the 12-item display digest. Resolved Markdown edges are byte-identical on supabase (3,058), n8n, pretix and discourse, and the failed Markdown reference count is unchanged (11,368 on supabase). A full supabase index is a median 16.176 s to 15.953 s (Hyperfine 2.0.0, 8 runs per build, two ABBA rounds, 0.223 s/1.4%, interquartile ranges not overlapping). Re-index Markdown-heavy projects after upgrading.
+
 - **`codegraph sessions` and `codegraph_sessions` can search history before a date.** A search could only look back a number of days (`--since`, `sinceDays`), so its best 100 hits always came from the newest matching sessions and older context could not be reached. `--until <date>` and `until` keep only docs before a date (read as UTC) or a timestamp that names its zone; together with `--since` they bound a window.
 
 - A background sync after editing a widely imported file no longer leaves the MCP daemon holding about 19 GB (n8n, one new export in a barrel imported from 335 files). Re-checking the importers built a native resolver per binding and the process kept about 2.5 MB of each; they now share one. That check went from 38.7 s to 0.5 s, and idle memory after the edit from 19.4 GB to 1.4 GB.
diff --git a/__tests__/fixtures/golden/payroll-go.dump b/__tests__/fixtures/golden/payroll-go.dump
index 7012d043da..cd7381ff6a 100644
--- a/__tests__/fixtures/golden/payroll-go.dump
+++ b/__tests__/fixtures/golden/payroll-go.dump
@@ -1,4 +1,4 @@
-== nodes (313)
+== nodes (309)
 {"id":"constant:03cf22f9cca66ee928171cceccbf44b1","kind":"constant","name":"LineEarning","qualified_name":"LineEarning","file_path":"internal/domain/payroll/payslip.go","language":"go","start_line":25,"end_line":25,"start_column":1,"end_column":35,"docstring":null,"signature":"= \"earning\"","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"constant:49f451a6950b1d7e90eb6cfe2776192b","kind":"constant","name":"LineDeduction","qualified_name":"LineDeduction","file_path":"internal/domain/payroll/payslip.go","language":"go","start_line":26,"end_line":26,"start_column":1,"end_column":37,"docstring":null,"signature":"= \"deduction\"","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"constant:56977e604248e3674f9296a2f68154bb","kind":"constant","name":"PayrollService_GetPayrollCycle_FullMethodName","qualified_name":"PayrollService_GetPayrollCycle_FullMethodName","file_path":"internal/gen/payrollpb/payroll_grpc.pb.go","language":"go","start_line":17,"end_line":17,"start_column":1,"end_column":93,"docstring":null,"signature":"= \"/payroll.v1.PayrollService/GetPayrollCycle\"","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
@@ -8,7 +8,7 @@
 {"id":"constant:c62a1da458c5f390b2ac8d4662f81801","kind":"constant","name":"PayrollService_ListPayslips_FullMethodName","qualified_name":"PayrollService_ListPayslips_FullMethodName","file_path":"internal/gen/payrollpb/payroll_grpc.pb.go","language":"go","start_line":18,"end_line":18,"start_column":1,"end_column":90,"docstring":null,"signature":"= \"/payroll.v1.PayrollService/ListPayslips\"","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"constant:ccc3400ce237825d2c42ef5fe177fe35","kind":"constant","name":"CycleOpen","qualified_name":"CycleOpen","file_path":"internal/domain/payroll/payslip.go","language":"go","start_line":9,"end_line":9,"start_column":1,"end_column":33,"docstring":null,"signature":"= \"open\"","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"constant:e8d10fecacdc9d2de71a3e3f7cd39d77","kind":"constant","name":"CycleClosed","qualified_name":"CycleClosed","file_path":"internal/domain/payroll/payslip.go","language":"go","start_line":10,"end_line":10,"start_column":1,"end_column":35,"docstring":null,"signature":"= \"closed\"","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
-{"id":"file:69f63e0581b8138f256b63d2aac60e8a","kind":"file","name":"README.md","qualified_name":"README.md","file_path":"README.md","language":"markdown","start_line":1,"end_line":96,"start_column":0,"end_column":0,"docstring":"A synthetic Go service reproducing the repo shape from issue #1500:  ·  refs: payslip.go, store.go, .pb.go, cycle.go, explore-allocation-1500.test.ts, payslip_builder.go, probe-allocation.mjs, allocation-fixtures.js","signature":null,"visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
+{"id":"file:69f63e0581b8138f256b63d2aac60e8a","kind":"file","name":"README.md","qualified_name":"README.md","file_path":"README.md","language":"markdown","start_line":1,"end_line":96,"start_column":0,"end_column":0,"docstring":"A synthetic Go service reproducing the repo shape from issue #1500:  ·  refs: payslip.go, store.go, .pb.go, cycle.go, explore-allocation-1500.test.ts, payslip_builder.go, probe-allocation.mjs, allocation-fixtures.js  ·  links: .pb.go, explore-allocation-1500.test.ts, allocation-fixtures.js, explore-budget-allocation.md","signature":null,"visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"file:cmd/payrolld/main.go","kind":"file","name":"main.go","qualified_name":"cmd/payrolld/main.go","file_path":"cmd/payrolld/main.go","language":"go","start_line":1,"end_line":36,"start_column":0,"end_column":0,"docstring":null,"signature":null,"visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"file:internal/domain/payroll/payslip.go","kind":"file","name":"payslip.go","qualified_name":"internal/domain/payroll/payslip.go","file_path":"internal/domain/payroll/payslip.go","language":"go","start_line":1,"end_line":160,"start_column":0,"end_column":0,"docstring":null,"signature":null,"visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"file:internal/gen/fkit/employee/contract.go","kind":"file","name":"contract.go","qualified_name":"internal/gen/fkit/employee/contract.go","file_path":"internal/gen/fkit/employee/contract.go","language":"go","start_line":1,"end_line":85,"start_column":0,"end_column":0,"docstring":null,"signature":null,"visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
@@ -116,7 +116,6 @@
 {"id":"import:0bd6a21b585b4de298027fb9855ca26a","kind":"import","name":"github.com/example/payroll-svc/internal/domain/payroll","qualified_name":"github.com/example/payroll-svc/internal/domain/payroll","file_path":"internal/usecase/payroll/prorate.go","language":"go","start_line":6,"end_line":6,"start_column":1,"end_column":57,"docstring":null,"signature":"\"github.com/example/payroll-svc/internal/domain/payroll\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:1150c8c775775f9f8560aa873017d153","kind":"import","name":"sort","qualified_name":"sort","file_path":"internal/usecase/payroll/cycle.go","language":"go","start_line":7,"end_line":7,"start_column":1,"end_column":7,"docstring":null,"signature":"\"sort\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:1ef8f8dc72d476dd57190a572c1f19e8","kind":"import","name":"time","qualified_name":"time","file_path":"internal/gen/fkit/timesheet/timesheet.go","language":"go","start_line":11,"end_line":11,"start_column":1,"end_column":7,"docstring":null,"signature":"\"time\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
-{"id":"import:20c50882bdafb89a0b54258fa936c5b2","kind":"import","name":"allocation-fixtures.js","qualified_name":"README.md::path:scripts/agent-eval/allocation-fixtures.js:79:49","file_path":"README.md","language":"markdown","start_line":79,"end_line":79,"start_column":49,"end_column":90,"docstring":null,"signature":"scripts/agent-eval/allocation-fixtures.js","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:2341305377f0bafe152c137e9466d659","kind":"import","name":"log","qualified_name":"log","file_path":"cmd/payrolld/main.go","language":"go","start_line":4,"end_line":4,"start_column":1,"end_column":6,"docstring":null,"signature":"\"log\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:2b0654627b2a83f4fa3e7b86866491c0","kind":"import","name":"context","qualified_name":"context","file_path":"internal/gen/fkit/employee/contract.go","language":"go","start_line":9,"end_line":9,"start_column":1,"end_column":10,"docstring":null,"signature":"\"context\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:3d7629cf02a4de5b41d0223adb5f3070","kind":"import","name":"time","qualified_name":"time","file_path":"internal/gen/fkit/employee/employee.go","language":"go","start_line":11,"end_line":11,"start_column":1,"end_column":7,"docstring":null,"signature":"\"time\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
@@ -139,13 +138,11 @@
 {"id":"import:65db04d07bd3a1a85e6702c070edbcf7","kind":"import","name":"context","qualified_name":"context","file_path":"internal/gen/fkit/employee/employee.go","language":"go","start_line":9,"end_line":9,"start_column":1,"end_column":10,"docstring":null,"signature":"\"context\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:66bc065f81b0782b430037fc979102cc","kind":"import","name":"time","qualified_name":"time","file_path":"internal/gen/fkit/payroll/payslip.go","language":"go","start_line":11,"end_line":11,"start_column":1,"end_column":7,"docstring":null,"signature":"\"time\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:68f937efbcbc4ebd082c1c11e72df0ab","kind":"import","name":"cycle.go","qualified_name":"README.md::path:cycle.go:49:50","file_path":"README.md","language":"markdown","start_line":49,"end_line":49,"start_column":50,"end_column":58,"docstring":null,"signature":"cycle.go","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
-{"id":"import:6a7e6476a09ea4596d045f1ae552a8f2","kind":"import","name":"explore-allocation-1500.test.ts","qualified_name":"README.md::path:__tests__/explore-allocation-1500.test.ts:52:15","file_path":"README.md","language":"markdown","start_line":52,"end_line":52,"start_column":15,"end_column":56,"docstring":null,"signature":"__tests__/explore-allocation-1500.test.ts","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:7147cac4b1745ea38b0bfa164a3a5468","kind":"import","name":"time","qualified_name":"time","file_path":"internal/gen/fkit/payroll/dto.go","language":"go","start_line":8,"end_line":8,"start_column":7,"end_column":13,"docstring":null,"signature":"\"time\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:7222e16172e240000e603eceb98f94f9","kind":"import","name":"database/sql","qualified_name":"database/sql","file_path":"internal/gen/fkit/payroll/payslip.go","language":"go","start_line":10,"end_line":10,"start_column":1,"end_column":15,"docstring":null,"signature":"\"database/sql\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:76a964b6134242af279f95c049ac84c5","kind":"import","name":"store.go","qualified_name":"README.md::path:internal/gen/fkit/payroll/store.go:87:56","file_path":"README.md","language":"markdown","start_line":87,"end_line":87,"start_column":56,"end_column":90,"docstring":null,"signature":"internal/gen/fkit/payroll/store.go","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:7afb422fcf48196342c2d44ba9df65b4","kind":"import","name":"context","qualified_name":"context","file_path":"internal/gen/fkit/payroll/store.go","language":"go","start_line":9,"end_line":9,"start_column":1,"end_column":10,"docstring":null,"signature":"\"context\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:85d6602214f6381a034f6034da409655","kind":"import","name":"database/sql","qualified_name":"database/sql","file_path":"internal/gen/fkit/employee/contract.go","language":"go","start_line":10,"end_line":10,"start_column":1,"end_column":15,"docstring":null,"signature":"\"database/sql\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
-{"id":"import:8808ae056445d4f7fae22fa62685c9a4","kind":"import","name":".pb.go","qualified_name":"README.md::path:.pb.go:41:15","file_path":"README.md","language":"markdown","start_line":41,"end_line":41,"start_column":15,"end_column":21,"docstring":null,"signature":".pb.go","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:8a55768bc75a7d6e26bd621aa388263c","kind":"import","name":"time","qualified_name":"time","file_path":"internal/gen/fkit/payroll/payroll_cycle.go","language":"go","start_line":11,"end_line":11,"start_column":1,"end_column":7,"docstring":null,"signature":"\"time\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:8ca292ed8417acda5c41ff30467e3188","kind":"import","name":"google.golang.org/protobuf/runtime/protoimpl","qualified_name":"google.golang.org/protobuf/runtime/protoimpl","file_path":"internal/gen/payrollpb/payroll.pb.go","language":"go","start_line":11,"end_line":11,"start_column":1,"end_column":57,"docstring":null,"signature":"protoimpl \"google.golang.org/protobuf/runtime/protoimpl\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:94d6b9da5b862536535fdb747dd8ef41","kind":"import","name":"google.golang.org/protobuf/reflect/protoreflect","qualified_name":"google.golang.org/protobuf/reflect/protoreflect","file_path":"internal/gen/payrollpb/payroll.pb.go","language":"go","start_line":10,"end_line":10,"start_column":1,"end_column":63,"docstring":null,"signature":"protoreflect \"google.golang.org/protobuf/reflect/protoreflect\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
@@ -171,7 +168,6 @@
 {"id":"import:e715312ec518c465211ed82ddce82285","kind":"import","name":"fmt","qualified_name":"fmt","file_path":"internal/usecase/payroll/payslip_builder.go","language":"go","start_line":5,"end_line":5,"start_column":1,"end_column":6,"docstring":null,"signature":"\"fmt\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:e9cab8103939c5ea907234285e597639","kind":"import","name":"time","qualified_name":"time","file_path":"internal/usecase/payroll/cycle.go","language":"go","start_line":8,"end_line":8,"start_column":1,"end_column":7,"docstring":null,"signature":"\"time\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:ee0a17b804d64444eaa8643521a20d48","kind":"import","name":"net/http","qualified_name":"net/http","file_path":"internal/transport/httpapi/router.go","language":"go","start_line":3,"end_line":3,"start_column":7,"end_column":17,"docstring":null,"signature":"\"net/http\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
-{"id":"import:f46fb6a4705f81701f5054f85a18d37f","kind":"import","name":"explore-budget-allocation.md","qualified_name":"README.md::path:docs/design/explore-budget-allocation.md:82:1","file_path":"README.md","language":"markdown","start_line":82,"end_line":82,"start_column":1,"end_column":41,"docstring":null,"signature":"docs/design/explore-budget-allocation.md","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:f779e8d1ccdf9fbef128be48f1cabe14","kind":"import","name":"errors","qualified_name":"errors","file_path":"internal/usecase/payroll/cycle.go","language":"go","start_line":5,"end_line":5,"start_column":1,"end_column":9,"docstring":null,"signature":"\"errors\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:fa23f47e6bf27f154f8044ad15346d18","kind":"import","name":"store.go","qualified_name":"README.md::path:store.go:38:45","file_path":"README.md","language":"markdown","start_line":38,"end_line":38,"start_column":45,"end_column":53,"docstring":null,"signature":"store.go","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"import:fe70ccaba78866b57f5239f961d3ea11","kind":"import","name":"fmt","qualified_name":"fmt","file_path":"internal/usecase/payroll/cycle.go","language":"go","start_line":6,"end_line":6,"start_column":1,"end_column":6,"docstring":null,"signature":"\"fmt\"","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
@@ -312,7 +308,7 @@
 {"id":"variable:6b7bef84822056845bdabeb41a821f0a","kind":"variable","name":"ErrCycleClosed","qualified_name":"ErrCycleClosed","file_path":"internal/usecase/payroll/cycle.go","language":"go","start_line":16,"end_line":16,"start_column":4,"end_column":58,"docstring":"ErrCycleClosed is returned when a cycle has already been finalized.","signature":"= errors.New(\"payroll cycle is closed\")","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"variable:9c3a0c9681a69504be5d3af6ddb5378c","kind":"variable","name":"file_payroll_v1_payroll_proto_goTypes","qualified_name":"file_payroll_v1_payroll_proto_goTypes","file_path":"internal/gen/payrollpb/payroll.pb.go","language":"go","start_line":132,"end_line":137,"start_column":4,"end_column":1,"docstring":null,"signature":"= []any{\n\t(*RunPayrollCycleRequest)(nil),\n\t(*RunPayrollCycleResponse)(nil),\n\t(*Payslip)(nil),\n\t(*Payro...","visibility":null,"is_exported":0,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
 {"id":"variable:baa4aee814b380ae99f1b1829407b106","kind":"variable","name":"ErrNoEmployees","qualified_name":"ErrNoEmployees","file_path":"internal/usecase/payroll/cycle.go","language":"go","start_line":19,"end_line":19,"start_column":4,"end_column":72,"docstring":"ErrNoEmployees is returned when a cycle resolves to an empty roster.","signature":"= errors.New(\"payroll cycle has no active employees\")","visibility":null,"is_exported":1,"is_async":0,"is_static":0,"is_abstract":0,"decorators":null,"type_parameters":null,"return_type":null}
-== edges (657)
+== edges (653)
 {"source":"file:69f63e0581b8138f256b63d2aac60e8a","target":"module:1be454da0953954aef45c525ee8f8b51","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"file:cmd/payrolld/main.go","target":"function:90eb51f51a3d9a397d4a53f26f2019aa","kind":"contains","metadata":null,"line":null,"col":null,"provenance":null}
 {"source":"file:cmd/payrolld/main.go","target":"import:0a9ee69fa4c64208200c3bebcbbf0b75","kind":"contains","metadata":null,"line":null,"col":null,"provenance":null}
@@ -847,8 +843,6 @@
 {"source":"module:1be454da0953954aef45c525ee8f8b51","target":"module:f8d63ed69e573ade27e2d1d4fc0ae8b4","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:39730d6601ee76ddcd5e78d50abfe5a2","target":"import:526c9118c077229729a7b9846c16882a","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:39730d6601ee76ddcd5e78d50abfe5a2","target":"import:68f937efbcbc4ebd082c1c11e72df0ab","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
-{"source":"module:39730d6601ee76ddcd5e78d50abfe5a2","target":"import:6a7e6476a09ea4596d045f1ae552a8f2","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
-{"source":"module:39730d6601ee76ddcd5e78d50abfe5a2","target":"import:8808ae056445d4f7fae22fa62685c9a4","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:39730d6601ee76ddcd5e78d50abfe5a2","target":"import:fa23f47e6bf27f154f8044ad15346d18","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:900ad55709598429050c36805696291a","target":"import:44b0fa4765bb8c262fb8b290698b9c05","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:900ad55709598429050c36805696291a","target":"import:e2b363aa11b1fe2c65cb016ea68a0948","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
@@ -872,8 +866,6 @@
 {"source":"module:a883d05f3bb8edb262fd18c8c2849417","target":"function:4827032314863eb2b99f791098f8668c","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:a883d05f3bb8edb262fd18c8c2849417","target":"function:8e554156c22d75e629b346ea4ed215d1","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:a883d05f3bb8edb262fd18c8c2849417","target":"function:c2b743a41c78c6d39eb292c4ecd1138d","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
-{"source":"module:a883d05f3bb8edb262fd18c8c2849417","target":"import:20c50882bdafb89a0b54258fa936c5b2","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
-{"source":"module:a883d05f3bb8edb262fd18c8c2849417","target":"import:f46fb6a4705f81701f5054f85a18d37f","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"module:f8d63ed69e573ade27e2d1d4fc0ae8b4","target":"import:76a964b6134242af279f95c049ac84c5","kind":"contains","metadata":null,"line":null,"col":null,"provenance":"heuristic"}
 {"source":"route:internal/transport/httpapi/router.go:10:GET:/v1/payroll/cycles/{cycleID}","target":"method:8baae5c5fb59db7a88c19bb295635d18","kind":"references","metadata":"{\"confidence\":0.9,\"resolvedBy\":\"exact-match\",\"refName\":\"GetCycle\"}","line":10,"col":0,"provenance":null}
 {"source":"route:internal/transport/httpapi/router.go:11:GET:/v1/payroll/cycles/{cycleID}/payslips","target":"method:6e0fe8d0272ee955601347cf37b5a383","kind":"references","metadata":"{\"confidence\":0.7,\"resolvedBy\":\"exact-match\",\"refName\":\"ListPayslips\"}","line":11,"col":0,"provenance":null}
@@ -2282,7 +2274,7 @@
 {"file_path":"internal/usecase/payroll/prorate.go","name":"to","kind":"param","node_id":null,"target_spec":null,"target_name":null,"exported_as":null,"export_form":null,"scope_start":34,"scope_end":39,"storage":null,"line":34}
 {"file_path":"internal/usecase/payroll/prorate.go","name":"window","kind":"local","node_id":null,"target_spec":null,"target_name":null,"exported_as":null,"export_form":null,"scope_start":11,"scope_end":24,"storage":null,"line":12}
 == files (21)
-{"path":"README.md","language":"markdown","node_count":37}
+{"path":"README.md","language":"markdown","node_count":33}
 {"path":"cmd/payrolld/main.go","language":"go","node_count":10}
 {"path":"internal/domain/payroll/payslip.go","language":"go","node_count":25}
 {"path":"internal/gen/fkit/employee/contract.go","language":"go","node_count":11}
diff --git a/__tests__/integration/full-pipeline.test.ts b/__tests__/integration/full-pipeline.test.ts
index 6a2fca222f..6d32099019 100644
--- a/__tests__/integration/full-pipeline.test.ts
+++ b/__tests__/integration/full-pipeline.test.ts
@@ -131,6 +131,45 @@ node scripts/release.mjs
     }
   });
 
+  it('resolves a full-index Markdown link after sync adds its target', async () => {
+    fs.mkdirSync(path.join(tempDir, 'docs'), { recursive: true });
+    fs.writeFileSync(
+      path.join(tempDir, 'README.md'),
+      `# Guide
+
+## Links
+
+See [Setup](docs/setup.md#install).
+`
+    );
+
+    const cg = await CodeGraph.init(tempDir);
+    try {
+      await cg.indexAll();
+      // The target is absent: the reference is kept (parked as failed), but no
+      // edge exists yet.
+      expect(cg.getNodesInFile('docs/setup.md')).toEqual([]);
+      const linksHeading = cg
+        .getNodesInFile('README.md')
+        .find((n) => n.kind === 'module' && n.name === 'Links')!;
+      expect(
+        cg.getOutgoingEdges(linksHeading.id)
+          .filter((e) => e.kind === 'imports')
+          .map((e) => cg.getNode(e.target)?.qualifiedName)
+      ).not.toContain('docs/setup.md#install');
+
+      fs.writeFileSync(path.join(tempDir, 'docs', 'setup.md'), '# Install\n\nInstall it.\n');
+      await cg.sync();
+
+      const install = cg
+        .getNodesInFile('docs/setup.md')
+        .find((n) => n.kind === 'module' && n.name === 'Install')!;
+      expect(cg.getIncomingEdges(install.id, ['imports']).some((e) => e.source === linksHeading.id)).toBe(true);
+    } finally {
+      cg.destroy();
+    }
+  });
+
   it('indexes Markdown template tables and resolves file-symbol references to implementation functions', async () => {
     fs.mkdirSync(path.join(tempDir, 'phases'), { recursive: true });
     fs.mkdirSync(path.join(tempDir, 'scripts'), { recursive: true });
diff --git a/__tests__/markdown-path-refs.test.ts b/__tests__/markdown-path-refs.test.ts
new file mode 100644
index 0000000000..3a65d179cd
--- /dev/null
+++ b/__tests__/markdown-path-refs.test.ts
@@ -0,0 +1,121 @@
+/**
+ * A Markdown path target whose basename no indexed file has cannot resolve to
+ * a file through the resolver's file-path arm. Its reference is still kept —
+ * the resolver's route/module/symbol arms may match it, and sync can retry it
+ * when a file appears later (#1240) — but its own import node only added a
+ * search child and a `contains` edge. A full index skips that node; sync keeps
+ * every node. Pruned targets stay in a separate, larger `links:` part of the
+ * file digest so a link beyond the 12-item display digest is still searchable.
+ */
+import { describe, it, expect } from 'vitest';
+import { extractFromSource } from '../src/extraction/tree-sitter';
+import type { MarkdownExtractorContext } from '../src/extraction/markdown-extractor';
+
+function context(prune: boolean, ...files: string[]): MarkdownExtractorContext {
+  return {
+    knownFileNames: new Set(files.map((file) => file.split('/').pop()!)),
+    pruneMissingTargets: prune,
+  };
+}
+
+const FULL_INDEX = context(true, 'docs/guide.md', 'src/widget.ts', 'scripts/exists.sh');
+const SYNC = context(false, 'docs/guide.md', 'src/widget.ts', 'scripts/exists.sh');
+
+const SOURCE = [
+  '# Guide',
+  '',
+  'Preamble about `createWidget`.',
+  '',
+  '## Links',
+  '',
+  '- [widget](../src/widget.ts)',
+  '- [missing](../src/missing.ts)',
+  '- [same name, other path](../apps/widget.ts#usage)',
+  '- [pricing](/pricing)',
+  '- [users route](/api/users/)',
+  '- [guide route](../guides/auth)',
+  '- [dotted route](api/users.json)',
+  '- [one](../src/one.ts)',
+  '- [two](../src/two.ts)',
+  '- [three](../src/three.ts)',
+  '- [four](../src/four.ts)',
+  '- [five](../src/five.ts)',
+  '- [six](../src/six.ts)',
+  '- [seven](../src/seven.ts)',
+  '- [eight](../src/eight.ts)',
+  '- [nine](../src/nine.ts)',
+  '- [ten](../src/ten.ts)',
+  '- [eleven](../src/eleven.ts)',
+  '- [twelve](../src/twelve.ts)',
+  '- [diagram](../assets/releaseblueprint.svg)',
+  '- [this section](#links)',
+  '',
+  'Mention `scripts/run.sh`, `scripts/widget.ts` and `src/widget.ts::createWidget`.',
+  'A missing symbol target: `src/missing.ts::createWidget`.',
+  '',
+  '```sh',
+  'bash scripts/missing.sh',
+  'bash scripts/exists.sh',
+  '```',
+].join('\n');
+
+function extract(withContext?: MarkdownExtractorContext) {
+  return extractFromSource('docs/guide.md', SOURCE, 'markdown', [], withContext);
+}
+
+function refs(withContext?: MarkdownExtractorContext): string[] {
+  return extract(withContext).unresolvedReferences.map((ref) => ref.referenceName);
+}
+
+function importTargets(withContext?: MarkdownExtractorContext): string[] {
+  return extract(withContext)
+    .nodes.filter((node) => node.kind === 'import')
+    .map((node) => node.qualifiedName);
+}
+
+describe('Markdown link-node pruning', () => {
+  it('keeps every reference and link node without a context', () => {
+    const names = refs();
+    expect(names).toContain('src/widget.ts');
+    expect(names).toContain('src/missing.ts');
+    expect(names).toContain('docs/scripts/run.sh');
+    expect(importTargets().some((qn) => qn.includes('missing.ts'))).toBe(true);
+  });
+
+  it('keeps the reference but skips the link node on a full index', () => {
+    const names = refs(FULL_INDEX);
+    // The reference survives so routes, modules and later syncs can match it.
+    expect(names).toContain('src/missing.ts');
+    expect(names).toContain('docs/scripts/run.sh');
+    expect(names).toContain('docs/scripts/missing.sh');
+    // The dead target's import node does not exist.
+    expect(importTargets(FULL_INDEX).some((qn) => qn.includes('missing.ts'))).toBe(false);
+    // A target whose basename is known keeps its node.
+    expect(importTargets(FULL_INDEX).some((qn) => qn.includes('src/widget.ts'))).toBe(true);
+  });
+
+  it('keeps every link node on an incremental sync', () => {
+    expect(importTargets(SYNC).some((qn) => qn.includes('missing.ts'))).toBe(true);
+  });
+
+  it('keeps routes and targets the resolver reaches by name', () => {
+    const names = refs(FULL_INDEX);
+    expect(names).toContain('apps/widget.ts#usage');
+    expect(names).toContain('docs/scripts/widget.ts');
+    expect(names).toContain('pricing');
+    expect(names).toContain('api/users/');
+    expect(names).toContain('guides/auth');
+    // A relative route with a dotted final segment is kept for name matching.
+    expect(names).toContain('docs/api/users.json');
+    expect(names).toContain('docs/src/widget.ts::createWidget');
+    expect(names).toContain('docs/guide.md#links');
+    expect(names).toContain('docs/scripts/exists.sh');
+  });
+
+  it('keeps a pruned target searchable beyond the display digest budget', () => {
+    const fileNode = extract(FULL_INDEX).nodes.find((node) => node.kind === 'file');
+    // The target is the 13th link, past the 12-item `refs:` budget.
+    expect(fileNode?.docstring).toContain('links:');
+    expect(fileNode?.docstring).toContain('releaseblueprint.svg');
+  });
+});
diff --git a/src/extraction/index.ts b/src/extraction/index.ts
index ce05f8e208..640219bd6a 100644
--- a/src/extraction/index.ts
+++ b/src/extraction/index.ts
@@ -2402,6 +2402,24 @@ export class ExtractionOrchestrator {
     }, skipStats);
     this.prepareLiquidThemeRoots(files);
     if (process.env.CODEGRAPH_SYNTH_TIMINGS) console.error(`[phase-timing] scan: ${Date.now() - tScan}ms (${files.length} files)`);
+
+    // Markdown link/path targets resolve through the file-path arm, which
+    // collects candidates by basename. Hand extraction that set so a path
+    // mention whose target file is absent creates no import node and no
+    // failed reference. Existing DB rows are included on a re-index so a ref
+    // whose target is still tracked (but gone from disk) resolves as before.
+    const knownFileNames = new Set<string>();
+    const rememberBasename = (file: string): void => {
+      const cut = Math.max(file.lastIndexOf('/'), file.lastIndexOf('\\'));
+      knownFileNames.add(cut >= 0 ? file.slice(cut + 1) : file);
+    };
+    for (const file of files) rememberBasename(file);
+    for (const file of this.queries.getAllFilePaths()) rememberBasename(file);
+    // A full index has the whole project in hand, so a relative file target
+    // with no matching basename is dead. An incremental sync re-extracts one
+    // file at a time and must keep the reference for a target added later
+    // (#1240), so indexFile() passes no context and keeps every target.
+    const extractionContext = { knownFileNames, pruneMissingTargets: true };
     /** Only meaningful when nothing was indexable — see IndexResult (#1502). */
     const skipSummary = (): Pick<IndexResult, 'filesSkippedUnsupported' | 'topUnsupportedExtensions'> => {
       let total = 0;
@@ -2498,6 +2516,7 @@ export class ExtractionOrchestrator {
         recycleInterval: WORKER_RECYCLE_INTERVAL,
         parseTimeoutMs: PARSE_TIMEOUT_MS,
         log,
+        sharedContext: extractionContext,
       });
       log(`Parse worker pool: ${poolSize} worker(s)`);
       // Bulk index: every core will be needed — spawn the whole pool now so
@@ -2538,7 +2557,7 @@ export class ExtractionOrchestrator {
     const parseFile = (filePath: string, content: string): Promise<ExtractionResult> => {
       const language = detectLanguage(filePath, content, overrides, this.rootDir);
       const names = this.frameworksForFile(filePath, frameworkNames);
-      if (!pool) return Promise.resolve(extractFromSource(filePath, content, language, names));
+      if (!pool) return Promise.resolve(extractFromSource(filePath, content, language, names, extractionContext));
       return pool.requestParse({ filePath, content, language, frameworkNames: names });
     };
 
diff --git a/src/extraction/markdown-extractor.ts b/src/extraction/markdown-extractor.ts
index 4695ea4be4..7037e14ec8 100644
--- a/src/extraction/markdown-extractor.ts
+++ b/src/extraction/markdown-extractor.ts
@@ -19,6 +19,27 @@ interface FenceState {
   lines: Array<{ text: string; line: number }>;
 }
 
+/** Extraction inputs the Markdown extractor needs beyond the file itself. */
+export interface MarkdownExtractorContext {
+  /**
+   * Basenames of every file the index contains. Markdown path mentions and
+   * links resolve through the file-path arm, which looks candidates up by
+   * basename; a target whose basename is absent cannot resolve to a file.
+   * Omitted by callers without an index (unit tests, single-file tooling),
+   * which keeps the old permissive behaviour.
+   */
+  knownFileNames?: ReadonlySet<string>;
+  /**
+   * Skip the per-link import node for a target whose basename no indexed file
+   * has. Set only for a full project index. The reference is always kept: the
+   * resolver still tries the target's route/module/symbol arms and sync can
+   * retry a failed reference when a file appears later (#1240). The link node
+   * is decoration (a search child and a `contains` edge), so dropping it
+   * loses no edge. Without this flag every target gets its node, as before.
+   */
+  pruneMissingTargets?: boolean;
+}
+
 /**
  * Lightweight Markdown extractor.
  *
@@ -35,10 +56,20 @@ export class MarkdownExtractor {
   private errors: ExtractionError[] = [];
   private headings: HeadingInfo[] = [];
   private referenceKeys = new Set<string>();
+  private knownFileNames?: ReadonlySet<string>;
+  private pruneMissingTargets: boolean;
+  /**
+   * Targets whose import node was skipped. Their references are still stored;
+   * this list feeds a separate, larger `links:` part of the file digest so a
+   * link beyond the display digest's 12-item budget still stays searchable.
+   */
+  private prunedTargets: string[] = [];
 
-  constructor(filePath: string, source: string) {
+  constructor(filePath: string, source: string, context: MarkdownExtractorContext = {}) {
     this.filePath = normalizeRelativePath(filePath);
     this.lines = source.split('\n');
+    this.knownFileNames = context.knownFileNames;
+    this.pruneMissingTargets = context.pruneMissingTargets === true;
   }
 
   extract(): ExtractionResult {
@@ -430,27 +461,31 @@ export class MarkdownExtractor {
       if (!normalizedTarget) continue;
 
       const column = match.index;
-      const label = stripInlineMarkdown(match[1] || target) || target;
-      const displayName = path.posix.basename(stripAnchor(normalizedTarget)) || label;
-      const nodeId = generateNodeId(this.filePath, 'import', `${normalizedTarget}:${lineNumber}:${column}`, lineNumber);
-      const node: Node = {
-        id: nodeId,
-        kind: 'import',
-        name: displayName,
-        qualifiedName: `${this.filePath}::link:${normalizedTarget}:${lineNumber}:${column}`,
-        filePath: this.filePath,
-        language: 'markdown',
-        signature: match[0],
-        docstring: label,
-        startLine: lineNumber,
-        endLine: lineNumber,
-        startColumn: column,
-        endColumn: column + match[0].length,
-        updatedAt: Date.now(),
-      };
+      if (this.shouldCreateLinkNode(normalizedTarget)) {
+        const label = stripInlineMarkdown(match[1] || target) || target;
+        const displayName = path.posix.basename(stripAnchor(normalizedTarget)) || label;
+        const nodeId = generateNodeId(this.filePath, 'import', `${normalizedTarget}:${lineNumber}:${column}`, lineNumber);
+        const node: Node = {
+          id: nodeId,
+          kind: 'import',
+          name: displayName,
+          qualifiedName: `${this.filePath}::link:${normalizedTarget}:${lineNumber}:${column}`,
+          filePath: this.filePath,
+          language: 'markdown',
+          signature: match[0],
+          docstring: label,
+          startLine: lineNumber,
+          endLine: lineNumber,
+          startColumn: column,
+          endColumn: column + match[0].length,
+          updatedAt: Date.now(),
+        };
 
-      this.nodes.push(node);
-      this.edges.push({ source: owner.id, target: nodeId, kind: 'contains', provenance: 'heuristic' });
+        this.nodes.push(node);
+        this.edges.push({ source: owner.id, target: nodeId, kind: 'contains', provenance: 'heuristic' });
+      } else {
+        this.prunedTargets.push(normalizedTarget);
+      }
       this.addReference(owner.id, normalizedTarget, 'imports', lineNumber, column);
     }
   }
@@ -466,24 +501,28 @@ export class MarkdownExtractor {
       const normalizedTarget = this.normalizeReference(raw);
       if (!normalizedTarget) continue;
 
-      const nodeId = generateNodeId(this.filePath, 'import', `${normalizedTarget}:${lineNumber}:${match.index}`, lineNumber);
-      const node: Node = {
-        id: nodeId,
-        kind: 'import',
-        name: path.posix.basename(stripAnchor(normalizedTarget)) || normalizedTarget,
-        qualifiedName: `${this.filePath}::path:${normalizedTarget}:${lineNumber}:${match.index}`,
-        filePath: this.filePath,
-        language: 'markdown',
-        signature: raw,
-        startLine: lineNumber,
-        endLine: lineNumber,
-        startColumn: match.index,
-        endColumn: match.index + raw.length,
-        updatedAt: Date.now(),
-      };
+      if (this.shouldCreateLinkNode(normalizedTarget)) {
+        const nodeId = generateNodeId(this.filePath, 'import', `${normalizedTarget}:${lineNumber}:${match.index}`, lineNumber);
+        const node: Node = {
+          id: nodeId,
+          kind: 'import',
+          name: path.posix.basename(stripAnchor(normalizedTarget)) || normalizedTarget,
+          qualifiedName: `${this.filePath}::path:${normalizedTarget}:${lineNumber}:${match.index}`,
+          filePath: this.filePath,
+          language: 'markdown',
+          signature: raw,
+          startLine: lineNumber,
+          endLine: lineNumber,
+          startColumn: match.index,
+          endColumn: match.index + raw.length,
+          updatedAt: Date.now(),
+        };
 
-      this.nodes.push(node);
-      this.edges.push({ source: owner.id, target: nodeId, kind: 'contains', provenance: 'heuristic' });
+        this.nodes.push(node);
+        this.edges.push({ source: owner.id, target: nodeId, kind: 'contains', provenance: 'heuristic' });
+      } else {
+        this.prunedTargets.push(normalizedTarget);
+      }
       this.addReference(owner.id, normalizedTarget, 'references', lineNumber, match.index);
     }
   }
@@ -500,8 +539,10 @@ export class MarkdownExtractor {
       for (const symbol of symbols) {
         const normalizedTarget = this.normalizeReference(`${filePart}::${symbol}`);
         if (!normalizedTarget) continue;
+        const createNode = createImportNode && this.shouldCreateLinkNode(normalizedTarget);
+        if (createImportNode && !createNode) this.prunedTargets.push(normalizedTarget);
 
-        if (createImportNode) {
+        if (createNode) {
           const nodeId = generateNodeId(this.filePath, 'import', `${normalizedTarget}:${lineNumber}:${match.index}`, lineNumber);
           const node: Node = {
             id: nodeId,
@@ -554,9 +595,8 @@ export class MarkdownExtractor {
       const raw = match[0]!;
       if (text.slice(match.index + raw.length, match.index + raw.length + 2) === '::') continue;
       const normalizedTarget = this.normalizeReference(raw);
-      if (normalizedTarget) {
-        this.addReference(owner.id, normalizedTarget, 'references', lineNumber, match.index);
-      }
+      if (!normalizedTarget) continue;
+      this.addReference(owner.id, normalizedTarget, 'references', lineNumber, match.index);
     }
   }
 
@@ -622,6 +662,37 @@ export class MarkdownExtractor {
     return `${normalized}${symbolPart ? `::${symbolPart}` : ''}${anchor}`;
   }
 
+  /**
+   * Whether a target should get its own import node on a full index. The
+   * resolver's file-path arm collects candidates by basename, so a target
+   * whose basename no file node has cannot resolve to a file. Its reference
+   * is still recorded (the resolver's route/module/symbol arms may match it,
+   * and sync can retry it when a file appears), but the link node only added a
+   * search child and a `contains` edge. Without a known-file set, or outside a
+   * full index, every target keeps its node.
+   */
+  private shouldCreateLinkNode(normalizedTarget: string): boolean {
+    if (!this.pruneMissingTargets || !this.knownFileNames) return true;
+    const [pathAndSymbol] = splitAnchor(normalizedTarget);
+    const [pathPart] = splitFileSymbol(pathAndSymbol);
+    if (!pathPart || pathPart === this.filePath) return true;
+    return this.knownFileNames.has(path.posix.basename(pathPart));
+  }
+
+  /** Pruned link targets for the file digest's separate `links:` part. */
+  private summarizePrunedTargets(): string[] {
+    const seen = new Set<string>();
+    const out: string[] = [];
+    for (const target of this.prunedTargets) {
+      const display = compactRefDisplay(target);
+      if (!display || seen.has(display)) continue;
+      seen.add(display);
+      out.push(display);
+      if (out.length >= 64) break;
+    }
+    return out;
+  }
+
   private buildDocstring(startLine: number, endLine: number): string | undefined {
     const text = this.lines
       .slice(Math.max(0, startLine - 1), Math.max(0, endLine))
@@ -659,9 +730,15 @@ export class MarkdownExtractor {
   private finalizeFileDigest(fileNode: Node): void {
     const intro = this.buildIntro();
     const refs = this.collectKeyReferences();
+    const links = this.summarizePrunedTargets();
     const parts: string[] = [];
     if (intro) parts.push(intro);
     if (refs.length > 0) parts.push(`refs: ${refs.join(', ')}`);
+    if (links.length > 0) {
+      let text = links.join(', ');
+      if (text.length > 800) text = `${text.slice(0, 797).trimEnd()}...`;
+      parts.push(`links: ${text}`);
+    }
     const digest = parts.join('  ·  ').trim();
     fileNode.docstring = digest || this.buildDocstring(1, Math.min(this.lines.length, 40));
   }
@@ -698,18 +775,20 @@ export class MarkdownExtractor {
   /**
    * The documents/symbols this file points at, de-duplicated and compacted
    * (basename + `::symbol`/`#anchor`) in document order. Self-anchors and pure
-   * in-page links are dropped. Bounded so the whole digest stays short enough
-   * to display.
+   * in-page links are dropped. Includes targets pruned from the graph, so a
+   * link to an unindexed asset still makes the file findable. Bounded so the
+   * whole digest stays short enough to display.
    */
   private collectKeyReferences(maxItems = 12, maxChars = 150): string[] {
     const seen = new Set<string>();
     const out: string[] = [];
     let budget = maxChars;
     for (const ref of this.unresolvedReferences) {
-      const [pathSym] = splitAnchor(ref.referenceName);
+      const referenceName = ref.referenceName;
+      const [pathSym] = splitAnchor(referenceName);
       const [pathPart] = splitFileSymbol(pathSym);
       if (!pathPart || pathPart === this.filePath) continue; // pure/self anchor
-      const display = compactRefDisplay(ref.referenceName);
+      const display = compactRefDisplay(referenceName);
       if (!display || seen.has(display)) continue;
       if (out.length >= maxItems) break;
       if (out.length > 0 && budget - display.length - 2 < 0) break;
diff --git a/src/extraction/parse-pool.ts b/src/extraction/parse-pool.ts
index 383666ae58..05b3ae8091 100644
--- a/src/extraction/parse-pool.ts
+++ b/src/extraction/parse-pool.ts
@@ -22,6 +22,7 @@
 
 import { Worker } from 'worker_threads';
 import type { Language, ExtractionResult } from '../types';
+import type { MarkdownExtractorContext } from './markdown-extractor';
 
 /**
  * Minimal worker surface the pool drives — satisfied by a real `worker_threads`
@@ -210,6 +211,11 @@ export interface ParseWorkerPoolOptions {
   loadSettleMs?: number;
   /** Optional verbose logger (the orchestrator's `[worker] …` logger). */
   log?: (msg: string) => void;
+  /**
+   * Extraction inputs every worker needs before its first parse (the
+   * index's known file basenames). Sent once per spawn, not per parse.
+   */
+  sharedContext?: MarkdownExtractorContext;
 }
 
 export class ParseWorkerPool {
@@ -236,6 +242,7 @@ export class ParseWorkerPool {
   private readonly createWorker: () => ParsePoolWorker;
   private readonly loadSettleMs: number;
   private readonly log: (msg: string) => void;
+  private readonly sharedContext?: MarkdownExtractorContext;
 
   constructor(opts: ParseWorkerPoolOptions) {
     this.languages = opts.languages;
@@ -244,6 +251,7 @@ export class ParseWorkerPool {
     this.parseTimeoutMs = opts.parseTimeoutMs ?? DEFAULT_PARSE_TIMEOUT_MS;
     this.loadSettleMs = opts.loadSettleMs ?? GRAMMAR_LOAD_SETTLE_MS;
     this.log = opts.log ?? (() => {});
+    this.sharedContext = opts.sharedContext;
     if (opts.createWorker) {
       this.createWorker = opts.createWorker;
     } else if (opts.workerScriptPath) {
@@ -320,7 +328,16 @@ export class ParseWorkerPool {
     w.on('error', (e) => { this.loadSettled(w); this.onWorkerGone(w, `${WORKER_DIED}: ${e?.message ?? 'unknown error'}`); });
     w.on('exit', (code) => { this.loadSettled(w); if (code !== 0) this.onWorkerGone(w, `${WORKER_DIED}: exited with code ${code}`); });
     // Readiness handshake; the worker replies 'grammars-loaded' and only then is idle.
-    w.postMessage({ type: 'load-grammars', languages: this.languages });
+    // The shared extraction context rides along, so a recycled worker gets it
+    // again without a per-parse clone.
+    w.postMessage({
+      type: 'load-grammars',
+      languages: this.languages,
+      knownFileNames: this.sharedContext?.knownFileNames
+        ? [...this.sharedContext.knownFileNames]
+        : undefined,
+      pruneMissingTargets: this.sharedContext?.pruneMissingTargets,
+    });
   }
 
   private onMessage(w: ParsePoolWorker, m: ParseWorkerMessage): void {
diff --git a/src/extraction/parse-worker.ts b/src/extraction/parse-worker.ts
index 4e30c35928..76bf578200 100644
--- a/src/extraction/parse-worker.ts
+++ b/src/extraction/parse-worker.ts
@@ -22,11 +22,20 @@ import { applyFrameworkExtracts } from './framework-extracts';
 import { mayDefineCppMacroMethods } from './languages/cpp-macro-methods';
 import type { Language, ExtractionResult } from '../types';
 
-parentPort!.on('message', async (msg: { type: string; id?: number; filePath?: string; content?: string; languages?: Language[]; frameworkNames?: string[]; language?: Language }) => {
+/**
+ * The index's known file basenames, for the Markdown extractor's path check.
+ * Sent once per worker spawn (the pool re-sends it to a recycled worker).
+ */
+let knownFileNames: Set<string> | undefined;
+let pruneMissingTargets: boolean | undefined;
+
+parentPort!.on('message', async (msg: { type: string; id?: number; filePath?: string; content?: string; languages?: Language[]; frameworkNames?: string[]; language?: Language; knownFileNames?: string[]; pruneMissingTargets?: boolean }) => {
   if (msg.type === 'load-grammars') {
     // Nothing to load since the wasm path was removed: grammars live in the
     // kernel binary. The handshake stays so the pool's readiness model
     // (spawned → ready → idle) is unchanged.
+    knownFileNames = msg.knownFileNames ? new Set(msg.knownFileNames) : undefined;
+    pruneMissingTargets = msg.pruneMissingTargets;
     parentPort!.postMessage({ type: 'grammars-loaded' });
   } else if (msg.type === 'parse') {
     const { id, filePath, content, frameworkNames } = msg;
@@ -67,7 +76,15 @@ parentPort!.on('message', async (msg: { type: string; id?: number; filePath?: st
           applyFrameworkExtracts(result, filePath!, content!, language, frameworkNames);
         }
       }
-      result ??= extractFromSource(filePath!, content!, language, frameworkNames);
+      result ??= extractFromSource(
+        filePath!,
+        content!,
+        language,
+        frameworkNames,
+        knownFileNames || pruneMissingTargets
+          ? { knownFileNames, pruneMissingTargets }
+          : undefined
+      );
 
       parentPort!.postMessage({ type: 'parse-result', id, result, parseMs: performance.now() - t0 });
     } catch (err) {
diff --git a/src/extraction/tree-sitter.ts b/src/extraction/tree-sitter.ts
index e4c043e633..1924540b6f 100644
--- a/src/extraction/tree-sitter.ts
+++ b/src/extraction/tree-sitter.ts
@@ -39,7 +39,7 @@ import { DfmExtractor } from './dfm-extractor';
 import { PASCAL_SYSTEM_NAMES } from './languages/pascal-system';
 import { VueExtractor } from './vue-extractor';
 import { MyBatisExtractor } from './mybatis-extractor';
-import { MarkdownExtractor } from './markdown-extractor';
+import { MarkdownExtractor, type MarkdownExtractorContext } from './markdown-extractor';
 import { CfmlExtractor } from './cfml-extractor';
 import { tryKernelExtract, takeDeferredPreParse, tryKernelBindings, attachBindingNodeIds } from './kernel';
 import { captureLiterals } from './literal-capture';
@@ -9857,7 +9857,8 @@ export function extractFromSource(
   filePath: string,
   source: string,
   language?: Language,
-  frameworkNames?: string[]
+  frameworkNames?: string[],
+  context?: MarkdownExtractorContext
 ): ExtractionResult {
   const detectedLanguage = language || detectLanguage(filePath, source);
   const fileExtension = path.extname(filePath).toLowerCase();
@@ -9891,7 +9892,7 @@ export function extractFromSource(
     result = extractor.extract();
   } else if (detectedLanguage === 'markdown') {
     // Use custom extractor for Markdown documentation structure and references
-    const extractor = new MarkdownExtractor(filePath, source);
+    const extractor = new MarkdownExtractor(filePath, source, context);
     result = extractor.extract();
   } else if (detectedLanguage === 'cfml' || detectedLanguage === 'cfscript') {
     // Custom extractor for CFML (.cfc/.cfm) — dialect-switches between the