scip-query 0.19.6 → 0.19.8

package/CHANGELOG.md

@@ -4,6 +4,43 @@ All notable changes to `scip-query` are documented here. This file starts at 0.1
 
 ## [Unreleased]
 
+## [0.19.8]
+
+### Complete agent evidence
+
+- Every descriptor-backed command now supports resumable output pages backed
+  by one immutable private snapshot. Pages report exact character totals,
+  bind cursors to the original invocation and content hash, and emit the exact
+  continuation command without rerunning a nondeterministic query.
+- Incomplete machine-readable and human pages identify themselves as
+  incomplete evidence. Generated project guidance requires agents to retrieve
+  every page before drawing a conclusion, changing evidence commands, or
+  reporting completion.
+
+### Diff-gate containment
+
+- CLI and Stop-hook gates now share a per-project single-flight lease, so
+  overlapping agents report the live owner instead of multiplying detector
+  work.
+- Gate evaluation runs in an owned child with a finite 60-second deadline, or
+  180 seconds with `--full`. Timeout terminates and reaps the child and fails
+  closed.
+- Historical finding reconciliation replays at most one comparison base per
+  foreground gate, runs only the detectors needed for that base, and leaves
+  deferred findings open with exact counts.
+
+### Security and operational hardening
+
+- Repository-controlled paths, tools, regular expressions, persisted records,
+  subprocesses, and output now cross explicit containment, size, time, and
+  trust boundaries. Terminal text is rendered inert, and destructive cache
+  operations require verified ownership.
+- Watchers and semantic mailboxes back off while idle, suppress redundant
+  refreshes, and preserve one canonical source identity across filesystem
+  aliases.
+- Production dependency audit and release preflight now reject high-severity
+  production advisories; the shipped production dependency tree is clean.
+
 ## [0.19.6]
 
 ### State and process resilience

package/README.md

@@ -34,15 +34,15 @@ Two layers, wired by `scip-query setup`:
 
 **Invoked** — the agent routes work through skills, each carrying its own short command list so it never navigates the full CLI:
 
-| Phase    | Skill                                            | Commands underneath (also usable directly)          |
-| -------- | ------------------------------------------------ | --------------------------------------------------- |
-| Orient   | `scip-explore`                                   | `system`, `trace`, `affected`, `call-graph`         |
-| Plan     | `scip-plan`                                      | `plan-context`, `change-surface`, `co-change`       |
-| Diagnose | `scip-diagnose`                                  | `files`, `trace`, `call-graph`, `outline`           |
-| Audit    | `scip-audit`                                     | `cleanup-plan --verify`, `dead`, `twin-drift`       |
-| Improve  | `scip-improve`                                   | `incomplete-migration`, `recent-duplicates`         |
-| Verify   | `scip-verify` (closeout) + the ambient diff gate | `diff-impact`, `diff-gate`, `health --baseline`     |
-| Set up   | `scip-setup`                                     | `doctor`, `setup`, `setup-hooks`, `setup-agent`     |
+| Phase    | Skill                                            | Commands underneath (also usable directly)      |
+| -------- | ------------------------------------------------ | ----------------------------------------------- |
+| Orient   | `scip-explore`                                   | `system`, `trace`, `affected`, `call-graph`     |
+| Plan     | `scip-plan`                                      | `plan-context`, `change-surface`, `co-change`   |
+| Diagnose | `scip-diagnose`                                  | `files`, `trace`, `call-graph`, `outline`       |
+| Audit    | `scip-audit`                                     | `cleanup-plan --verify`, `dead`, `twin-drift`   |
+| Improve  | `scip-improve`                                   | `incomplete-migration`, `recent-duplicates`     |
+| Verify   | `scip-verify` (closeout) + the ambient diff gate | `diff-impact`, `diff-gate`, `health --baseline` |
+| Set up   | `scip-setup`                                     | `doctor`, `setup`, `setup-hooks`, `setup-agent` |
 
 The consolidated skills retain the former specialist lenses as routed
 scenarios: API impact and formal/performance planning live in `scip-plan`;
@@ -119,8 +119,9 @@ scip-query similar <closest-symbol>
 # After an extraction or migration: find sites that still contain old logic
 scip-query incomplete-migration
 
-# Before declaring the work complete: refresh the index and gate the diff
-scip-query reindex && scip-query diff-gate --json
+# Before declaring the work complete: gate the diff. Reindex only when status
+# reports stale and no live watcher or hook refresh is already responsible.
+scip-query diff-gate --json
 ```
 
 For a repository-wide cleanup pass:
@@ -285,7 +286,7 @@ used, `diff-gate` reports exact incomplete-coverage counts and keeps findings
 conservatively unsuppressed. The wire schemas and merge rules are documented
 in [`docs/COMMITTED_RECORD_COMPATIBILITY.md`](docs/COMMITTED_RECORD_COMPATIBILITY.md).
 
-**12. Measure whether the gate is earning its keep.** Every completed `diff-gate` run, including JSON and installed Stop-hook runs, writes each finding transition to its own committed `.scipquery/events/*.json` file. Independent branches add independent paths instead of editing one shared ledger file, so ordinary event writes do not create merge conflicts. Each event stores the immutable Git commit used as its comparison base. A finding is a verified fix when it disappears under that same comparison—either directly or after scip-query cleanly replays the original base against a newer committed `HEAD`. Merely committing the finding cannot clear it: if replay still finds it, the outcome stays open; if the worktree is dirty or Git cannot reproduce the base, verification waits. A suppressed finding was noise or an accepted trade-off:
+**12. Measure whether the gate is earning its keep.** Every completed `diff-gate` run, including JSON and installed Stop-hook runs, writes each finding transition to its own committed `.scipquery/events/*.json` file. Independent branches add independent paths instead of editing one shared ledger file, so ordinary event writes do not create merge conflicts. Each event stores the immutable Git commit used as its comparison base. A finding is a verified fix when it disappears under that same comparison—either directly or after scip-query cleanly replays the original base against a newer committed `HEAD`. Merely committing the finding cannot clear it: if replay still finds it, the outcome stays open; if the worktree is dirty or Git cannot reproduce the base, verification waits. Historical reconciliation is deliberately incremental: one run replays at most one stored comparison base, reports the exact deferred base and finding counts, and leaves every deferred finding open for a later gate. A suppressed finding was noise or an accepted trade-off:
 
 ```bash
 scip-query effectiveness --since 30d
@@ -297,7 +298,15 @@ echo        14      10     2           1     0      1           83%        0.8
 new-dead    6       5      0           1     0      0           100%       0.3
 ```
 
-`precision` is verified fixed ÷ (verified fixed + suppressed). `moved` separates rename churn, while `unverified` is reserved for legacy or otherwise non-comparable resolutions that lack replay proof. Run diff-gate once to record the finding and again after the repair; a pre-commit rerun uses the same base directly, while a clean post-commit run automatically replays the stored base. Filter with `--check <name>`, window with `--since 30d|12w|<ISO date>`, and get machine-readable output with `--json`. Because the event files are committed, the numbers survive re-clones and aggregate across every machine and agent working the repo. Current event files carry an additive v1 discriminator, stable semantic identity, and writer version; existing unversioned files remain readable. `effectiveness` reports accepted and omitted record counts when history is partial, and cross-HEAD verification defers fixes rather than trusting an incomplete lifecycle. Legacy `.scipquery/ledger/events.jsonl` records remain readable and are migrated to individual files on the next gate write only when every non-empty line is compatible; otherwise the source ledger is preserved. Historical cross-`HEAD` events without stored comparison evidence remain unverified rather than being reclassified speculatively. Standalone health/cleanup commands are not yet outcome-tracked because they do not all expose a complete-scan contract.
+`precision` is verified fixed ÷ (verified fixed + suppressed). `moved` separates rename churn, while `unverified` is reserved for legacy or otherwise non-comparable resolutions that lack replay proof. Run diff-gate once to record the finding and again after the repair; a pre-commit rerun uses the same base directly, while clean post-commit runs advance through stored bases incrementally. Filter with `--check <name>`, window with `--since 30d|12w|<ISO date>`, and get machine-readable output with `--json`. Because the event files are committed, the numbers survive re-clones and aggregate across every machine and agent working the repo. Current event files carry an additive v1 discriminator, stable semantic identity, and writer version; existing unversioned files remain readable. `effectiveness` reports accepted and omitted record counts when history is partial, and cross-HEAD verification defers fixes rather than trusting an incomplete lifecycle. Legacy `.scipquery/ledger/events.jsonl` records remain readable and are migrated to individual files on the next gate write only when every non-empty line is compatible; otherwise the source ledger is preserved. Historical cross-`HEAD` events without stored comparison evidence remain unverified rather than being reclassified speculatively. Standalone health/cleanup commands are not yet outcome-tracked because they do not all expose a complete-scan contract.
+
+`diff-gate` is also single-flight per project: a second CLI or Stop-hook gate
+returns the live owner's PID and start time instead of duplicating the same
+CPU-heavy work. The gate runs in an owned child process with a 60-second
+deadline, or 180 seconds with `--full`; timeout terminates and reaps that child
+and fails the gate explicitly. Operators may set
+`SCIP_QUERY_DIFF_GATE_TIMEOUT_MS` to a positive millisecond value, capped at
+10 minutes.
 
 The health report also keeps a worktree-local repeat counter in `evidence.db`.
 A logical observation is one completed detector evaluation named by an
@@ -403,7 +412,8 @@ reports Rust's final durable/worker semantic selection and lifecycle state.
 The status read is passive; the setup health audit may make a semantic request
 that wakes rust-analyzer, after which the helper exits on clean idle.
 It also installs/refreshes skills, configures project-local hooks unless
-skipped, checks indexer readiness, attempts configured indexer remediation,
+skipped, checks indexer readiness, performs explicitly approved pinned indexer
+remediation,
 refreshes the index, smoke-tests representative command families, writes
 `docs/scip-query/health-dossier.md` and `.json` when the optional health pass is
 selected, reports the health score and items needing attention, and seeds
@@ -414,7 +424,9 @@ explicitly). After setup,
 `scip-audit` confirms raw signals and `scip-improve` keeps
 fixing the worst confirmed items until no safe confirmed cleanup remains. Use
 `scip-query setup --git-hook` when you also want a local pre-commit diff gate.
-CI setup is intentionally separate.
+Non-interactive setup and ordinary reindex report missing global tools without
+installing them; pass `--install-missing` only when that operation may install
+the reviewed immutable package versions. CI setup is intentionally separate.
 
 Setup classifies every change by where its facts belong:
 
@@ -832,6 +844,7 @@ Query results are filtered through the project's `.gitignore`. If none exists, c
 - [Agent Guide](docs/AGENT_GUIDE.md): goal-oriented workflows for tracing, planning, cleanup, quality checks, and change verification.
 - [Command Reference](docs/COMMAND_REFERENCE.md): generated command syntax, descriptions, and options.
 - [CLI JSON output contract](docs/CLI_JSON_OUTPUT.md): versioned envelopes, compatibility rules, and schema.
+- [Security model](docs/SECURITY_MODEL.md): untrusted-checkout boundaries, authority flags, input budgets, and complete-output pagination.
 - [Programmatic API](docs/API.md): using the query functions from TypeScript.
 - [Historical plans](https://github.com/PlunderStruck/scip-query/tree/main/docs/plans): implementation notes and completed cleanup plans.
 

package/dist/augment-vue-worker.js

@@ -1,2 +1,2 @@
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+import{c as t}from"./chunk-3ZSJ3PWF.js";import"./chunk-IF6FP6B2.js";import"./chunk-C5Q44Q5D.js";import"./chunk-46XGSFNI.js";import{writeFileSync as s}from"fs";import{workerData as o}from"worker_threads";var r=o;try{let e=t({projectRoot:r.projectRoot,dbPath:r.dbPath,tsconfig:r.tsconfig,vueFiles:r.vueFiles,tasks:r.tasks});s(r.resultPath,JSON.stringify({version:1,runId:r.runId,workerId:r.workerId,taskIds:r.taskIds,ok:!0,result:e}))}catch(e){s(r.resultPath,JSON.stringify({version:1,runId:r.runId,workerId:r.workerId,taskIds:r.taskIds,ok:!1,error:e instanceof Error?e.message:String(e)}))}
 //# sourceMappingURL=augment-vue-worker.js.map

package/dist/chunk-2465DLHK.js

@@ -0,0 +1,3 @@
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package/dist/{chunk-FKGN4A4E.js → chunk-2U3OLUNJ.js}

@@ -1,4 +1,4 @@
-import{c as R}from"./chunk-XVJ3V7LM.js";import{a as _,d as f}from"./chunk-WMXRRBII.js";import{d as l}from"./chunk-ZTTISZ7J.js";import{o as u,p,q as a}from"./chunk-7LABSJSR.js";import{H as m}from"./chunk-B5MHCHP3.js";import{a as d}from"./chunk-64MNV6AB.js";function $(e,o={}){let{scope:n,limit:r}=o,i=new R(e),t=D([...x(e,n),...O(e,i,n)]);return y(t),r?t.slice(0,r):t}function x(e,o){let n=[];for(let r of S(e,o)){if(e.isIgnored(r.barrel_path)||e.isIgnored(r.original_path)||f(e,r.barrel_path)||m(e,r.barrel_path)&&a(e,r.barrel_path).length===0)continue;let i=N(e,r),t=i?.barrel_consumers??0,s=i?.direct_consumers??0;t!==0||s!==0||n.push({barrelFile:r.barrel_path,symbol:r.symbol,shortName:l(r.symbol),originalFile:r.original_path,barrelConsumers:t,directConsumers:s,...b(e,r.barrel_path)})}return n}function S(e,o){let n=o?"AND barrel_d.relative_path LIKE ?":"",r=o?[`%${o}%`]:[];return e.all(`SELECT DISTINCT
+import{c as R}from"./chunk-2SNGN6U4.js";import{a as _,d as f}from"./chunk-LP3ARJKF.js";import{d as l}from"./chunk-RA3AYNWP.js";import{o as u,p,q as a}from"./chunk-MZZBAITE.js";import{O as m}from"./chunk-JORHF5AL.js";import{a as d}from"./chunk-64MNV6AB.js";function $(e,o={}){let{scope:n,limit:r}=o,i=new R(e),t=D([...x(e,n),...O(e,i,n)]);return y(t),r?t.slice(0,r):t}function x(e,o){let n=[];for(let r of S(e,o)){if(e.isIgnored(r.barrel_path)||e.isIgnored(r.original_path)||f(e,r.barrel_path)||m(e,r.barrel_path)&&a(e,r.barrel_path).length===0)continue;let i=N(e,r),t=i?.barrel_consumers??0,s=i?.direct_consumers??0;t!==0||s!==0||n.push({barrelFile:r.barrel_path,symbol:r.symbol,shortName:l(r.symbol),originalFile:r.original_path,barrelConsumers:t,directConsumers:s,...b(e,r.barrel_path)})}return n}function S(e,o){let n=o?"AND barrel_d.relative_path LIKE ?":"",r=o?[`%${o}%`]:[];return e.all(`SELECT DISTINCT
       barrel_d.id AS barrel_doc_id,
       barrel_d.relative_path AS barrel_path,
       gs.id AS symbol_id,
@@ -58,4 +58,4 @@ import{c as R}from"./chunk-XVJ3V7LM.js";import{a as _,d as f}from"./chunk-WMXRRB
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package/dist/{chunk-UUJBLG6J.js → chunk-33KUO7CG.js}

@@ -1,2 +1,2 @@
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package/dist/{chunk-N3SE646F.js → chunk-33XTHFKR.js}

@@ -1,2 +1,2 @@
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package/dist/{chunk-WXAAURU7.js → chunk-3EDFLQ6A.js}

@@ -1,3 +1,3 @@
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+//# sourceMappingURL=chunk-3EDFLQ6A.js.map

package/dist/chunk-3ZSJ3PWF.js

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+    SELECT
+      d.relative_path AS relativePath,
+      der.start_line AS startLine,
+      der.end_line AS endLine,
+      der.symbol_id AS symbolId,
+      gs.display_name AS displayName
+    FROM defn_enclosing_ranges der
+    JOIN documents d ON d.id = der.document_id
+    JOIN global_symbols gs ON gs.id = der.symbol_id
+    ORDER BY d.relative_path, (der.end_line - der.start_line) DESC
+  `).all(),r=new Map;for(let t of n){let o=r.get(t.relativePath);o||(o={containingByLine:new Map,starts:[]},r.set(t.relativePath,o)),o.starts.push({line:t.startLine,symbolId:t.symbolId,displayName:t.displayName});for(let i=t.startLine;i<=t.endLine;i++)o.containingByLine.set(i,{symbolId:t.symbolId,displayName:t.displayName})}for(let t of r.values())t.starts.sort((o,i)=>o.line-i.line);return r}function fe(e,n,r,t){let o=0,i=e.length-1;for(;o<=i;){let a=Math.floor((o+i)/2);e[a].line<n?o=a+1:i=a-1}let s=null;for(let a of[i,o]){let u=e[a];if(!u||u.displayName!==t)continue;let c=Math.abs(u.line-n);c>r||(!s||c<s.distance)&&(s={distance:c,symbolId:u.symbolId})}return s?.symbolId??null}function N(e,n){let r=Se(n),t=e.prepare("SELECT id FROM global_symbols WHERE symbol = ?"),o=new Map;return{get(i){if(o.has(i))return o.get(i)??null;let s=he(t,r,n,i);return o.set(i,s),s}}}function _(e,n,r,t,o){if(e.fileName.endsWith(".vue")){let 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package/dist/{chunk-G4UQL4CP.js → chunk-43KC6EQZ.js}

@@ -1,2 +1,2 @@
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package/dist/{chunk-NQLSSVOB.js → chunk-464PLI5O.js}

@@ -1,2 +1,2 @@
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package/dist/chunk-46XGSFNI.js

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package/dist/{chunk-NN4ZIRPK.js → chunk-47BU5Z4T.js}

@@ -1,8 +1,8 @@
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+import{a as T,c as E,g as L,h as D}from"./chunk-4YTUWQ6M.js";import{j as O,o as A}from"./chunk-WANA4KAQ.js";import{d as H}from"./chunk-KMVGRIO2.js";import{c as _}from"./chunk-2SNGN6U4.js";import{d as C,e as F}from"./chunk-RA3AYNWP.js";import{a as w}from"./chunk-MZZBAITE.js";var J=5;function ae(e,t={}){let{base:a="HEAD",minContainment:o=.7,minCallees:r=3,minSiteCoverage:n=.4,maxHelpers:c=Number.POSITIVE_INFINITY,limit:m=20,scanLimit:g}=t,f=t.semantic!==!1,s=t.diffPlan??E(e,{base:a}),l={available:s.note!==T,base:a,changedFiles:s.changedFiles,helpersChecked:0,skipped:[],findings:[]};if(!l.available||s.changedFiles.length===0)return l;let x=new _(e),k=new Set(s.changedFiles),$=new Map(s.renamedFiles.map(i=>[i.to,i.from])),j=t.baseContentAt??L(e.config.projectRoot,a,D(s)),h=Z(x,k,$,j);if(h.length===0)return l;let R=h.slice(0,c);h.length>c&&(l.note=`helper scoring capped at ${c} of ${h.length} new symbols`);let q=x.calleeMap(R,{semantic:f}),B=R.map(i=>({def:i,callees:A((q.get(i.symbolId)??[]).map(p=>p.symbol))})),V=O(e),M,G=()=>(M??=V.calleeIndex({minCallees:Math.min(3,r),scanLimit:g,semantic:f}),M);for(let{def:i,callees:p}of B){let d=C(i.symbol);if(p.size<r){l.skipped.push({helperShortName:d,helperFile:i.relativePath,reason:`fewer than ${r} meaningful callees \u2014 too small to score`});continue}let P=G(),N=Y(p,P);if(N===0){l.skipped.push({helperShortName:d,helperFile:i.relativePath,reason:"helper callee pattern is all project-wide infrastructure \u2014 too generic to score"});continue}let b=Q(e,i.symbolId);if(b.length===0){l.skipped.push({helperShortName:d,helperFile:i.relativePath,reason:"no references yet \u2014 covered by the new-dead check"});continue}l.helpersChecked+=1;let I=K({candidateIndex:P,changed:k,helperCallees:p,helperFile:i.relativePath,helperSymbol:i.symbol,minContainment:o,minSiteCoverage:n,migratedFiles:b});I.length!==0&&(I.sort((u,S)=>z(S.migrationScope)-z(u.migrationScope)||S.containment-u.containment||S.siteCoverage-u.siteCoverage||u.file.localeCompare(S.file)),l.findings.push({helperSymbol:i.symbol,helperShortName:d,helperFile:i.relativePath,helperShape:"specific-callee-cluster",helperCalleeCount:p.size,specificHelperCalleeCount:N,migratedFiles:b.sort(),leftovers:I.slice(0,J)}))}return l.findings.sort((i,p)=>(p.leftovers[0]?.containment??0)-(i.leftovers[0]?.containment??0)||i.helperFile.localeCompare(p.helperFile)),l.findings=l.findings.slice(0,m),l}function K(e){let t=[],a=U(e.helperSymbol,e.helperFile,e.migratedFiles),o=new Set;for(let r of e.helperCallees)for(let n of e.candidateIndex.candidateIndexesByCallee.get(r)??[])o.add(n);for(let r of o){let n=e.candidateIndex.corpus[r];if(n.symbol===e.helperSymbol||e.changed.has(n.file)||n.callees.has(e.helperSymbol))continue;let c=H(e.helperCallees,n.callees);if(c<e.minContainment)continue;let m=[...e.helperCallees].filter(s=>n.callees.has(s)),g=n.callees.size===0?0:m.length/n.callees.size;if(g<e.minSiteCoverage||!m.some(s=>(e.candidateIndex.docFreq.get(s)??0)<=e.candidateIndex.ubiquityThreshold))continue;let f=W(a,n.symbol,n.file);t.push({symbol:n.symbol,shortName:C(n.symbol),file:n.file,...f,containment:c,siteCoverage:g,uniqueSiteCalleeCount:Math.max(0,n.callees.size-m.length),sharedCallees:m.map(C).sort()})}return t}function z(e){return e==="same-scope"?2:e==="unknown"?1:0}function U(e,t,a){let o=new Set([...y(t),...v(F(e))]);for(let r of a)for(let n of y(r))o.add(n);return o}function W(e,t,a){let o=new Set([...y(a),...v(F(t))]);if(e.size===0||o.size===0)return{migrationScope:"unknown",migrationScopeReasons:["insufficient path/name tokens to infer migration scope"]};let r=[...o].filter(n=>e.has(n)).sort();return r.length>0?{migrationScope:"same-scope",migrationScopeReasons:[`shares migration-scope token(s): ${r.slice(0,5).join(", ")}`]}:{migrationScope:"possible-subtype",migrationScopeReasons:["no path/name tokens shared with the helper or already migrated files"]}}var X=new Set(["app","apps","common","component","components","helper","helpers","index","lib","package","packages","page","pages","route","routes","service","services","shared","spec","src","test","tests","util","utils"]);function y(e){return v(e.replace(/\.[^.]+$/,""))}function v(e){return e.replace(/([a-z0-9])([A-Z])/g,"$1 $2").toLowerCase().split(/[^a-z0-9]+/).filter(t=>t.length>1&&!X.has(t))}function Y(e,t){let a=0;for(let o of e)(t.docFreq.get(o)??0)<=t.ubiquityThreshold&&(a+=1);return a}function Z(e,t,a,o){return e.productionCallableDefinitions({files:[...t],requireFunctionLikeSymbol:!0}).filter(r=>{if(!t.has(r.relativePath))return!1;let n=a.get(r.relativePath)??r.relativePath,c=o(n);return c===null||!new RegExp(`\\b${w(r.leaf)}\\b`).test(c)})}function Q(e,t){return e.all(`SELECT DISTINCT ref_d.relative_path
      FROM mentions m
      JOIN chunks c ON m.chunk_id = c.id
      JOIN documents ref_d ON c.document_id = ref_d.id
      WHERE m.symbol_id = ?
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+//# sourceMappingURL=chunk-47BU5Z4T.js.map

package/dist/chunk-4BV4QAZJ.js

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