From 9953c16bd60351f3a7772aa22e3e1ac88cc1ae9a Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 11:22:01 -0400
Subject: [PATCH 01/10] ensure filter paths are resolved relative to project

---
 src/command/render/filters.ts | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 1081b5fc6e..4c22305566 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -85,7 +85,7 @@ import { quartoConfig } from "../../core/quarto.ts";
 import { metadataNormalizationFilterActive } from "./normalize.ts";
 import { kCodeAnnotations } from "../../format/html/format-html-shared.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
-import { relative } from "../../deno_ral/path.ts";
+import { join, relative } from "../../deno_ral/path.ts";
 import { citeIndexFilterParams } from "../../project/project-cites.ts";
 import { debug } from "../../deno_ral/log.ts";
 import { kJatsSubarticle } from "../../format/jats/format-jats-types.ts";
@@ -746,14 +746,17 @@ export async function resolveFilters(
     .filter((f) => f !== "quarto") // remove quarto marker
     .map((filter, i) => {
       if (isFilterEntryPoint(filter)) {
-        return filter; // send entry-point-style filters unchanged
+        return {
+          ...filter,
+          path: join(options.project.dir, filter.path),
+        }; // send entry-point-style filters unchanged
       }
       const at = quartoLoc > i ? kQuartoPre : kQuartoPost;
       const result: QuartoFilterEntryPoint = typeof filter === "string"
         ? {
           "at": at,
           "type": filter.endsWith(".lua") ? "lua" : "json",
-          "path": filter,
+          "path": join(options.project.dir, filter),
         }
         : {
           "at": at,

From 8d41d30e15be4a1bb2cbb05604c0d6e370f5e5d7 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 11:22:54 -0400
Subject: [PATCH 02/10] regressiont test

---
 .../04/08/fix-filter-project-paths/.gitignore |  1 +
 .../08/fix-filter-project-paths/_quarto.yml   | 21 +++++++++++++++++++
 .../04/08/fix-filter-project-paths/about.qmd  |  5 +++++
 .../04/08/fix-filter-project-paths/index.qmd  |  9 ++++++++
 .../04/08/fix-filter-project-paths/root.lua   |  4 ++++
 .../04/08/fix-filter-project-paths/styles.css |  1 +
 6 files changed, 41 insertions(+)
 create mode 100644 tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/.gitignore
 create mode 100644 tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/_quarto.yml
 create mode 100644 tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/about.qmd
 create mode 100644 tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/index.qmd
 create mode 100644 tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/root.lua
 create mode 100644 tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/styles.css

diff --git a/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/.gitignore b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/.gitignore
new file mode 100644
index 0000000000..075b2542af
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/.gitignore
@@ -0,0 +1 @@
+/.quarto/
diff --git a/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/_quarto.yml b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/_quarto.yml
new file mode 100644
index 0000000000..e8cfb5f72c
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/_quarto.yml
@@ -0,0 +1,21 @@
+project:
+  type: website
+
+website:
+  title: "fix-filter-project-paths"
+  navbar:
+    left:
+      - href: index.qmd
+        text: Home
+      - about.qmd
+
+format:
+  html:
+    theme:
+      - cosmo
+      - brand
+    css: styles.css
+    toc: true
+
+
+
diff --git a/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/about.qmd b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/about.qmd
new file mode 100644
index 0000000000..07c5e7f9d1
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/about.qmd
@@ -0,0 +1,5 @@
+---
+title: "About"
+---
+
+About this site
diff --git a/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/index.qmd b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/index.qmd
new file mode 100644
index 0000000000..7b8e67ae3a
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/index.qmd
@@ -0,0 +1,9 @@
+---
+title: "fix-filter-project-paths"
+filters:
+  - /root.lua
+---
+
+This is a Quarto website.
+
+To learn more about Quarto websites visit <https://quarto.org/docs/websites>.
diff --git a/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/root.lua b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/root.lua
new file mode 100644
index 0000000000..d20aba2d1a
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/root.lua
@@ -0,0 +1,4 @@
+function Pandoc(doc)
+  -- we just need to make sure this runs
+  return doc
+end
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/styles.css b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/styles.css
new file mode 100644
index 0000000000..2ddf50c7b4
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/fix-filter-project-paths/styles.css
@@ -0,0 +1 @@
+/* css styles */

From 28e2cf10c95779629548dc59bf6cc4f9ca7bdef1 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 13:13:07 -0400
Subject: [PATCH 03/10] carry path type information throughout extension
 resolution

---
 src/command/render/filters.ts | 217 +++++++++++++++++++++++-----------
 src/config/types.ts           |  21 +++-
 src/extension/extension.ts    |   2 +-
 3 files changed, 166 insertions(+), 74 deletions(-)

diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 4c22305566..d4e8a40354 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -62,6 +62,8 @@ import {
   isFilterEntryPoint,
   QuartoFilter,
   QuartoFilterEntryPoint,
+  QuartoFilterEntryPointQualified,
+  QuartoFilterEntryPointQualifiedFull,
 } from "../../config/types.ts";
 import { QuartoFilterSpec } from "./types.ts";
 import { Metadata } from "../../config/types.ts";
@@ -85,7 +87,7 @@ import { quartoConfig } from "../../core/quarto.ts";
 import { metadataNormalizationFilterActive } from "./normalize.ts";
 import { kCodeAnnotations } from "../../format/html/format-html-shared.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
-import { join, relative } from "../../deno_ral/path.ts";
+import { extname, join, relative, resolve } from "../../deno_ral/path.ts";
 import { citeIndexFilterParams } from "../../project/project-cites.ts";
 import { debug } from "../../deno_ral/log.ts";
 import { kJatsSubarticle } from "../../format/jats/format-jats-types.ts";
@@ -95,6 +97,7 @@ import { pythonExec } from "../../core/jupyter/exec.ts";
 import { kTocIndent } from "../../config/constants.ts";
 import { isWindows } from "../../deno_ral/platform.ts";
 import { tinyTexBinDir } from "../../tools/impl/tinytex-info.ts";
+import { warn } from "log";
 
 const kQuartoParams = "quarto-params";
 
@@ -716,7 +719,7 @@ const kQuartoCiteProcMarker = "citeproc";
 
 // NB: this mutates `pandoc.citeproc`
 export async function resolveFilters(
-  filters: QuartoFilter[],
+  filtersParam: QuartoFilter[],
   options: PandocOptions,
   pandoc: FormatPandoc,
 ): Promise<QuartoFilterSpec | undefined> {
@@ -729,8 +732,10 @@ export async function resolveFilters(
   quartoFilters.push(quartoMainFilter());
 
   // Resolve any filters that are provided by an extension
-  filters = await resolveFilterExtension(options, filters);
-  let quartoLoc = filters.findIndex((filter) => filter === kQuartoFilterMarker);
+  const filters = await resolveFilterExtension(options, filtersParam);
+  let quartoLoc = filters.findIndex((filter) =>
+    filter.type === kQuartoFilterMarker
+  );
   if (quartoLoc === -1) {
     quartoLoc = Infinity; // if no quarto marker, put our filters at the beginning
   }
@@ -742,31 +747,28 @@ export async function resolveFilters(
   // if 'quarto' is not in the filter, all declarations go to the kQuartoPre entry point
   //
   // (note that citeproc will in all cases run last)
-  const entryPoints: QuartoFilterEntryPoint[] = filters
-    .filter((f) => f !== "quarto") // remove quarto marker
+
+  // citeproc at the very end so all other filters can interact with citations
+
+  // remove special filter markers
+  const fullFilters = filters.filter((filter) =>
+    filter.type !== kQuartoCiteProcMarker && filter.type !== kQuartoFilterMarker
+  ) as QuartoFilterEntryPointQualifiedFull[];
+
+  const entryPoints: QuartoFilterEntryPoint[] = fullFilters
     .map((filter, i) => {
-      if (isFilterEntryPoint(filter)) {
-        return {
-          ...filter,
-          path: join(options.project.dir, filter.path),
-        }; // send entry-point-style filters unchanged
-      }
-      const at = quartoLoc > i ? kQuartoPre : kQuartoPost;
-      const result: QuartoFilterEntryPoint = typeof filter === "string"
-        ? {
-          "at": at,
-          "type": filter.endsWith(".lua") ? "lua" : "json",
-          "path": join(options.project.dir, filter),
-        }
-        : {
-          "at": at,
-          ...filter,
-        };
+      const at = filter.at === "__quarto-auto"
+        ? (quartoLoc > i ? kQuartoPre : kQuartoPost)
+        : filter.at;
+
+      const result: QuartoFilterEntryPoint = {
+        "at": at,
+        "type": filter.type,
+        "path": filter.path.path,
+      };
       return result;
     });
 
-  // citeproc at the very end so all other filters can interact with citations
-  filters = filters.filter((filter) => filter !== kQuartoCiteProcMarker);
   const citeproc = citeMethod(options) === kQuartoCiteProcMarker;
   if (citeproc) {
     // If we're explicitely adding the citeproc filter, turn off
@@ -847,60 +849,133 @@ function pdfEngine(options: PandocOptions): string {
   return pdfEngine;
 }
 
+// Resolve any filters that are provided by an extension
 async function resolveFilterExtension(
   options: PandocOptions,
   filters: QuartoFilter[],
-): Promise<QuartoFilter[]> {
-  // Resolve any filters that are provided by an extension
-  const results: (QuartoFilter | QuartoFilter[])[] = [];
-  const getFilter = async (filter: QuartoFilter) => {
-    // Look for extension names in the filter list and result them
-    // into the filters provided by the extension
-    if (
-      filter !== kQuartoFilterMarker && filter !== kQuartoCiteProcMarker &&
-      typeof filter === "string"
-    ) {
-      // The filter string points to an executable file which exists
-      if (existsSync(filter) && !Deno.statSync(filter).isDirectory) {
-        return filter;
+): Promise<QuartoFilterEntryPointQualified[]> {
+  const results:
+    (QuartoFilterEntryPointQualified | QuartoFilterEntryPointQualified[])[] =
+      [];
+
+  // Look for extension names in the filter list and result them
+  // into the filters provided by the extension
+  const getFilter = async (
+    filter: QuartoFilter,
+  ): Promise<
+    QuartoFilterEntryPointQualified | QuartoFilterEntryPointQualified[]
+  > => {
+    if (filter === kQuartoFilterMarker || filter === kQuartoCiteProcMarker) {
+      return { type: filter };
+    }
+    if (typeof filter !== "string") {
+      // deno-lint-ignore no-explicit-any
+      if ((filter as any).at) {
+        const entryPoint = filter as QuartoFilterEntryPoint;
+        return {
+          ...entryPoint,
+          path: {
+            type: "relative",
+            path: entryPoint.path,
+          },
+        };
+      } else {
+        return {
+          at: "__quarto-auto",
+          type: filter.type,
+          path: {
+            type: "relative",
+            path: filter.path,
+          },
+        };
       }
+    }
 
-      const extensions = await options.services.extension?.find(
-        filter,
-        options.source,
-        "filters",
-        options.project?.config,
-        options.project?.dir,
-      ) || [];
-
-      // Filter this list of extensions
-      const filteredExtensions = filterExtensions(
-        extensions || [],
-        filter,
-        "filter",
+    // The filter string points to an executable file which exists
+    if (existsSync(filter) && !Deno.statSync(filter).isDirectory) {
+      const type = extname(filter) !== "lua" ? "json" : "lua";
+      return {
+        at: "__quarto-auto",
+        type,
+        path: {
+          type: "absolute",
+          path: resolve(filter),
+        },
+      };
+    }
+
+    const extensions = await options.services.extension?.find(
+      filter,
+      options.source,
+      "filters",
+      options.project?.config,
+      options.project?.dir,
+    ) || [];
+
+    if (extensions.length === 0) {
+      // There were no extensions matching this name,
+      // this should not happen
+      //
+      // Previously, we allowed it to pass, we're warning now and dropping
+      warn(
+        `No extensions matching name but filter (${filter}) is a string that isn't an existing path or quarto or citeproc. Ignoring`,
       );
-      // Return any contributed plugins
-      if (filteredExtensions.length > 0) {
-        // This matches an extension, use the contributed filters
-        const filters = extensions[0].contributes.filters;
-        if (filters) {
-          return filters;
-        } else {
-          return filter;
-        }
-      } else if (extensions.length > 0) {
-        // There was a matching extension with this name, but
-        // it was filtered out, just hide the filter altogether
-        return [];
-      } else {
-        // There were no extensions matching this name, just allow it
-        // through
-        return filter;
-      }
-    } else {
-      return filter;
+      return [];
     }
+
+    // Filter this list of extensions
+    const filteredExtensions = filterExtensions(
+      extensions || [],
+      filter,
+      "filter",
+    );
+
+    if (filteredExtensions.length === 0) {
+      // There was a matching extension with this name, but
+      // it was filtered out, just hide the filter altogether
+      return [];
+    }
+
+    // Return any contributed plugins
+    // This matches an extension, use the contributed filters
+    const filters = extensions[0].contributes.filters;
+    if (!filters) {
+      warn(
+        `No extensions matching name but filter (${filter}) is a string that isn't an existing path or quarto or citeproc. Ignoring`,
+      );
+      return [];
+    }
+
+    // our extension-finding service returns absolute paths
+    // so any paths below will be "type": "absolute"
+    // and need no conversion
+
+    return filters.map((f) => {
+      if (typeof f === "string") {
+        const isExistingFile = existsSync(f) && !Deno.statSync(f).isDirectory;
+        const type = (isExistingFile && extname(f) !== ".lua") ? "json" : "lua";
+        return {
+          at: "__quarto-auto",
+          type,
+          path: {
+            type: "absolute",
+            path: f,
+          },
+        };
+      }
+
+      return {
+        ...f,
+        // deno-lint-ignore no-explicit-any
+        at: (f as any).at ?? "__quarto-auto",
+        path: {
+          type: "absolute",
+          path: f.path,
+        },
+      };
+    });
   };
+
   for (const filter of filters) {
     const r = await getFilter(filter);
     results.push(r);
diff --git a/src/config/types.ts b/src/config/types.ts
index 8754526782..2a10678b3e 100644
--- a/src/config/types.ts
+++ b/src/config/types.ts
@@ -277,6 +277,11 @@ export interface FormatDependency {
   resources?: DependencyFile[];
 }
 
+type QualifiedPath = {
+  path: string;
+  type: "relative" | "project" | "absolute";
+};
+
 export interface DependencyFile {
   name: string;
   path: string;
@@ -350,7 +355,19 @@ export type PandocFilter = {
   path: string;
 };
 
-export type QuartoFilterEntryPoint = PandocFilter & { "at": string };
+export type QuartoFilterEntryPoint = PandocFilter & { at: string };
+
+export type QuartoFilterEntryPointQualifiedFull = {
+  type: "json" | "lua";
+  at: string;
+  path: QualifiedPath;
+};
+export type QuartoFilterSpecialEntryPoint = {
+  type: "citeproc" | "quarto";
+};
+export type QuartoFilterEntryPointQualified =
+  | QuartoFilterEntryPointQualifiedFull
+  | QuartoFilterSpecialEntryPoint;
 
 export type QuartoFilter = string | PandocFilter | QuartoFilterEntryPoint;
 
@@ -457,7 +474,7 @@ export interface Format {
 
 export interface LightDarkBrand {
   [kLight]?: Brand;
-  [kDark]?: Brand
+  [kDark]?: Brand;
 }
 
 export interface FormatRender {
diff --git a/src/extension/extension.ts b/src/extension/extension.ts
index c9d3650cf9..e045c1354a 100644
--- a/src/extension/extension.ts
+++ b/src/extension/extension.ts
@@ -230,7 +230,7 @@ export function filterExtensions(
   extensionId: string,
   type: string,
 ) {
-  if (extensions && extensions.length > 0) {
+  if (extensions.length > 0) {
     // First see if there are now built it (quarto organization)
     // filters that we previously provided by quarto-ext and
     // filter those out

From 5cfe6e027fc72c9ef929f21b5b03ad2e735499b7 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 13:24:14 -0400
Subject: [PATCH 04/10] include period in extension string test

---
 src/command/render/filters.ts | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index d4e8a40354..ab5da2e74b 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -87,7 +87,7 @@ import { quartoConfig } from "../../core/quarto.ts";
 import { metadataNormalizationFilterActive } from "./normalize.ts";
 import { kCodeAnnotations } from "../../format/html/format-html-shared.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
-import { extname, join, relative, resolve } from "../../deno_ral/path.ts";
+import { extname, relative, resolve } from "../../deno_ral/path.ts";
 import { citeIndexFilterParams } from "../../project/project-cites.ts";
 import { debug } from "../../deno_ral/log.ts";
 import { kJatsSubarticle } from "../../format/jats/format-jats-types.ts";
@@ -891,9 +891,9 @@ async function resolveFilterExtension(
       }
     }
 
-    // The filter string points to an executable file which exists
+    // The filter string points to a file which exists
     if (existsSync(filter) && !Deno.statSync(filter).isDirectory) {
-      const type = extname(filter) !== "lua" ? "json" : "lua";
+      const type = extname(filter) !== ".lua" ? "json" : "lua";
       return {
         at: "__quarto-auto",
         type,

From 43a5cc5016671cef6e267290a41c48450582b86a Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 13:55:16 -0400
Subject: [PATCH 05/10] preserve and resolve relative, project, and absolute
 paths properly

---
 src/command/render/filters.ts | 66 ++++++++++++++++++++++++-----------
 1 file changed, 45 insertions(+), 21 deletions(-)

diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index ab5da2e74b..51b5826edd 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -87,7 +87,7 @@ import { quartoConfig } from "../../core/quarto.ts";
 import { metadataNormalizationFilterActive } from "./normalize.ts";
 import { kCodeAnnotations } from "../../format/html/format-html-shared.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
-import { extname, relative, resolve } from "../../deno_ral/path.ts";
+import { dirname, extname, relative, resolve } from "../../deno_ral/path.ts";
 import { citeIndexFilterParams } from "../../project/project-cites.ts";
 import { debug } from "../../deno_ral/log.ts";
 import { kJatsSubarticle } from "../../format/jats/format-jats-types.ts";
@@ -755,6 +755,17 @@ export async function resolveFilters(
     filter.type !== kQuartoCiteProcMarker && filter.type !== kQuartoFilterMarker
   ) as QuartoFilterEntryPointQualifiedFull[];
 
+  const resolvePath = (filter: QuartoFilterEntryPointQualifiedFull["path"]) => {
+    switch (filter.type) {
+      case "absolute":
+        return filter.path;
+      case "relative":
+        return resolve(dirname(options.source), filter.path);
+      case "project":
+        return resolve(options.project.dir, filter.path);
+    }
+  };
+
   const entryPoints: QuartoFilterEntryPoint[] = fullFilters
     .map((filter, i) => {
       const at = filter.at === "__quarto-auto"
@@ -764,7 +775,7 @@ export async function resolveFilters(
       const result: QuartoFilterEntryPoint = {
         "at": at,
         "type": filter.type,
-        "path": filter.path.path,
+        "path": resolvePath(filter.path),
       };
       return result;
     });
@@ -869,24 +880,24 @@ async function resolveFilterExtension(
       return { type: filter };
     }
     if (typeof filter !== "string") {
+      const fileType: "project" | "relative" =
+        extname(filter.path).startsWith("/") ? "project" : "relative";
+      const path = {
+        type: fileType,
+        path: filter.path,
+      };
       // deno-lint-ignore no-explicit-any
       if ((filter as any).at) {
         const entryPoint = filter as QuartoFilterEntryPoint;
         return {
           ...entryPoint,
-          path: {
-            type: "relative",
-            path: entryPoint.path,
-          },
+          path,
         };
       } else {
         return {
           at: "__quarto-auto",
           type: filter.type,
-          path: {
-            type: "relative",
-            path: filter.path,
-          },
+          path,
         };
       }
     }
@@ -912,15 +923,31 @@ async function resolveFilterExtension(
       options.project?.dir,
     ) || [];
 
+    const fallthroughResult = () => {
+      const filterType: "json" | "lua" = extname(filter) !== ".lua"
+        ? "json"
+        : "lua";
+      const pathType: "project" | "relative" = filter.startsWith("/")
+        ? "project"
+        : "relative";
+
+      return {
+        at: "__quarto-auto",
+        type: filterType,
+        path: {
+          type: pathType,
+          path: filter,
+        },
+      };
+    };
+
     if (extensions.length === 0) {
       // There were no extensions matching this name,
-      // this should not happen
-      //
-      // Previously, we allowed it to pass, we're warning now and dropping
-      warn(
-        `No extensions matching name but filter (${filter}) is a string that isn't an existing path or quarto or citeproc. Ignoring`,
-      );
-      return [];
+      // but the filter is a string that isn't an existing path
+      // this indicates that the filter is meant to be interpreted
+      // as a project- or file-relative path
+
+      return fallthroughResult();
     }
 
     // Filter this list of extensions
@@ -940,10 +967,7 @@ async function resolveFilterExtension(
     // This matches an extension, use the contributed filters
     const filters = extensions[0].contributes.filters;
     if (!filters) {
-      warn(
-        `No extensions matching name but filter (${filter}) is a string that isn't an existing path or quarto or citeproc. Ignoring`,
-      );
-      return [];
+      return fallthroughResult();
     }
 
     // our extension-finding service returns absolute paths

From 79b7b635999434d6f419404d9d30947d8f4e5052 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 13:58:34 -0400
Subject: [PATCH 06/10] more path fixes

---
 src/command/render/filters.ts | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 51b5826edd..40b5375761 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -59,7 +59,6 @@ import { PandocOptions } from "./types.ts";
 import {
   Format,
   FormatPandoc,
-  isFilterEntryPoint,
   QuartoFilter,
   QuartoFilterEntryPoint,
   QuartoFilterEntryPointQualified,
@@ -87,7 +86,13 @@ import { quartoConfig } from "../../core/quarto.ts";
 import { metadataNormalizationFilterActive } from "./normalize.ts";
 import { kCodeAnnotations } from "../../format/html/format-html-shared.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
-import { dirname, extname, relative, resolve } from "../../deno_ral/path.ts";
+import {
+  dirname,
+  extname,
+  join,
+  relative,
+  resolve,
+} from "../../deno_ral/path.ts";
 import { citeIndexFilterParams } from "../../project/project-cites.ts";
 import { debug } from "../../deno_ral/log.ts";
 import { kJatsSubarticle } from "../../format/jats/format-jats-types.ts";
@@ -762,7 +767,7 @@ export async function resolveFilters(
       case "relative":
         return resolve(dirname(options.source), filter.path);
       case "project":
-        return resolve(options.project.dir, filter.path);
+        return resolve(join(options.project.dir, filter.path));
     }
   };
 
@@ -880,8 +885,9 @@ async function resolveFilterExtension(
       return { type: filter };
     }
     if (typeof filter !== "string") {
-      const fileType: "project" | "relative" =
-        extname(filter.path).startsWith("/") ? "project" : "relative";
+      const fileType: "project" | "relative" = filter.path.startsWith("/")
+        ? "project"
+        : "relative";
       const path = {
         type: fileType,
         path: filter.path,

From 3980cfbf6385d7de9e27c32d8e045ca7c1fcb316 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 14:11:15 -0400
Subject: [PATCH 07/10] resolve project-relative shortcodes

---
 src/command/render/filters.ts | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 40b5375761..67f209deb1 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -607,7 +607,11 @@ async function quartoFilterParams(
   }
   const shortcodes = format.render[kShortcodes];
   if (shortcodes !== undefined) {
-    params[kShortcodes] = shortcodes;
+    params[kShortcodes] = shortcodes.map((p) => {
+      if (p.startsWith("/")) {
+        return resolve(join(options.project.dir, p));
+      }
+    });
   }
   const extShortcodes = await extensionShortcodes(options);
   if (extShortcodes) {

From 3bc84439dd2eaaf93070f9099ce0afd67d8defaa Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 14:13:00 -0400
Subject: [PATCH 08/10] regression test

---
 .../2025/04/08/project-shortcode-paths/_quarto.yml     |  0
 .../2025/04/08/project-shortcode-paths/shortcode.lua   |  5 +++++
 .../04/08/project-shortcode-paths/subdir/hello.qmd     | 10 ++++++++++
 3 files changed, 15 insertions(+)
 create mode 100644 tests/docs/smoke-all/2025/04/08/project-shortcode-paths/_quarto.yml
 create mode 100644 tests/docs/smoke-all/2025/04/08/project-shortcode-paths/shortcode.lua
 create mode 100644 tests/docs/smoke-all/2025/04/08/project-shortcode-paths/subdir/hello.qmd

diff --git a/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/_quarto.yml b/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/_quarto.yml
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/shortcode.lua b/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/shortcode.lua
new file mode 100644
index 0000000000..e4753eec53
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/shortcode.lua
@@ -0,0 +1,5 @@
+return {
+    ['my-shortcode'] = function(args, kwargs, meta) 
+        return pandoc.Str("Hello from Shorty!")
+        end
+    }
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/subdir/hello.qmd b/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/subdir/hello.qmd
new file mode 100644
index 0000000000..87eeca199f
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/08/project-shortcode-paths/subdir/hello.qmd
@@ -0,0 +1,10 @@
+---
+title: "Hello"
+format: html
+shortcodes:
+  - /shortcode.lua
+---
+
+# Hello, world!
+
+{{< my-shortcode >}}

From 7f65fdaf97287efd9d6ad8209703ceaf10ae0e66 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 14:24:26 -0400
Subject: [PATCH 09/10] fix else condition

---
 src/command/render/filters.ts | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 67f209deb1..5ec3876de3 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -610,6 +610,8 @@ async function quartoFilterParams(
     params[kShortcodes] = shortcodes.map((p) => {
       if (p.startsWith("/")) {
         return resolve(join(options.project.dir, p));
+      } else {
+        return p;
       }
     });
   }

From 6b7bb1fdf7d3303ce75c66a9c2dbd86af47c37d4 Mon Sep 17 00:00:00 2001
From: Carlos Scheidegger <carlos.scheidegger@rstudio.com>
Date: Tue, 8 Apr 2025 16:20:25 -0400
Subject: [PATCH 10/10] extensions return fully-qualified filter declarations
 to avoid double-appending project paths

---
 src/command/preview/preview.ts |  37 ++++-
 src/command/render/filters.ts  |  45 +++---
 src/command/render/pandoc.ts   |  11 +-
 src/config/types.ts            |  24 ++-
 src/core/qualified-path.ts     | 257 +++------------------------------
 src/extension/extension.ts     |  59 ++++++--
 6 files changed, 159 insertions(+), 274 deletions(-)

diff --git a/src/command/preview/preview.ts b/src/command/preview/preview.ts
index 6c8bdab0e3..f07df8a39f 100644
--- a/src/command/preview/preview.ts
+++ b/src/command/preview/preview.ts
@@ -57,7 +57,11 @@ import { renderFormats } from "../render/render-contexts.ts";
 import { renderResultFinalOutput } from "../render/render.ts";
 import { replacePandocArg } from "../render/flags.ts";
 
-import { Format, isPandocFilter } from "../../config/types.ts";
+import {
+  Format,
+  isPandocFilter,
+  isQuartoFilterEntryPointQualifiedFull,
+} from "../../config/types.ts";
 import {
   kPdfJsInitialPath,
   pdfJsBaseDir,
@@ -467,17 +471,34 @@ export async function renderForPreview(
   extensionFiles.push(...renderResult.files.reduce(
     (extensionFiles: string[], file: RenderResultFile) => {
       const shortcodes = file.format.render.shortcodes || [];
-      const filters = (file.format.pandoc.filters || []).map((filter) =>
-        isPandocFilter(filter) ? filter.path : filter
-      );
+      const filters = (file.format.pandoc.filters || []).map((filter) => {
+        if (isPandocFilter(filter)) {
+          return filter.path;
+        }
+        if (isQuartoFilterEntryPointQualifiedFull(filter)) {
+          switch (filter.path.type) {
+            case "absolute":
+              return filter.path.path;
+            case "relative":
+              return join(dirname(file.input), filter.path.path);
+            case "project-relative":
+              return join(
+                project?.dir ?? dirname(file.input),
+                filter.path.path,
+              );
+          }
+        }
+        return filter;
+      });
       const ipynbFilters = file.format.execute["ipynb-filters"] || [];
       [...shortcodes, ...filters.map((filter) => filter), ...ipynbFilters]
         .forEach((extensionFile) => {
           if (!isAbsolute(extensionFile)) {
-            const extensionFullPath = join(dirname(file.input), extensionFile);
-            if (existsSync(extensionFullPath)) {
-              extensionFiles.push(normalizePath(extensionFullPath));
-            }
+            extensionFile = join(dirname(file.input), extensionFile);
+          }
+          // const extensionFullPath = join(dirname(file.input), extensionFile);
+          if (existsSync(extensionFile)) {
+            extensionFiles.push(normalizePath(extensionFile));
           }
         });
       return extensionFiles;
diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 5ec3876de3..33ae6bc0e8 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -65,7 +65,7 @@ import {
   QuartoFilterEntryPointQualifiedFull,
 } from "../../config/types.ts";
 import { QuartoFilterSpec } from "./types.ts";
-import { Metadata } from "../../config/types.ts";
+import { Metadata, QualifiedPath } from "../../config/types.ts";
 import { kProjectType } from "../../project/types.ts";
 import { bibEngine } from "../../config/pdf.ts";
 import { rBinaryPath, resourcePath } from "../../core/resources.ts";
@@ -772,7 +772,7 @@ export async function resolveFilters(
         return filter.path;
       case "relative":
         return resolve(dirname(options.source), filter.path);
-      case "project":
+      case "project-relative":
         return resolve(join(options.project.dir, filter.path));
     }
   };
@@ -891,13 +891,18 @@ async function resolveFilterExtension(
       return { type: filter };
     }
     if (typeof filter !== "string") {
-      const fileType: "project" | "relative" = filter.path.startsWith("/")
-        ? "project"
-        : "relative";
-      const path = {
-        type: fileType,
-        path: filter.path,
-      };
+      const path: QualifiedPath = (() => {
+        if (typeof filter.path !== "string") {
+          const result = filter.path;
+          return result;
+        }
+        const fileType: "project-relative" | "relative" =
+          filter.path.startsWith("/") ? "project-relative" : "relative";
+        return {
+          type: fileType,
+          path: filter.path,
+        };
+      })();
       // deno-lint-ignore no-explicit-any
       if ((filter as any).at) {
         const entryPoint = filter as QuartoFilterEntryPoint;
@@ -939,8 +944,8 @@ async function resolveFilterExtension(
       const filterType: "json" | "lua" = extname(filter) !== ".lua"
         ? "json"
         : "lua";
-      const pathType: "project" | "relative" = filter.startsWith("/")
-        ? "project"
+      const pathType: "project-relative" | "relative" = filter.startsWith("/")
+        ? "project-relative"
         : "relative";
 
       return {
@@ -999,15 +1004,21 @@ async function resolveFilterExtension(
           },
         };
       }
-
+      if (typeof f.path === "string") {
+        return {
+          ...f,
+          // deno-lint-ignore no-explicit-any
+          at: (f as any).at ?? "__quarto-auto",
+          path: {
+            type: "absolute",
+            path: f.path,
+          },
+        };
+      }
       return {
         ...f,
-        // deno-lint-ignore no-explicit-any
         at: (f as any).at ?? "__quarto-auto",
-        path: {
-          type: "absolute",
-          path: f.path,
-        },
+        path: f.path,
       };
     });
   };
diff --git a/src/command/render/pandoc.ts b/src/command/render/pandoc.ts
index 158e271402..8919e2ad1f 100644
--- a/src/command/render/pandoc.ts
+++ b/src/command/render/pandoc.ts
@@ -207,6 +207,7 @@ import { isWindows } from "../../deno_ral/platform.ts";
 import { appendToCombinedLuaProfile } from "../../core/performance/perfetto-utils.ts";
 import { makeTimedFunctionAsync } from "../../core/performance/function-times.ts";
 import { walkJson } from "../../core/json.ts";
+import { asRawPath } from "../../core/qualified-path.ts";
 
 // in case we are running multiple pandoc processes
 // we need to make sure we capture all of the trace files
@@ -919,11 +920,19 @@ export async function runPandoc(
     allDefaults.filters = allDefaults.filters.map((filter) => {
       if (typeof filter === "string") {
         return pandocMetadataPath(filter);
-      } else {
+      } else if (typeof filter.path === "string") {
         return {
           type: filter.type,
           path: pandocMetadataPath(filter.path),
         };
+      } else {
+        return {
+          type: filter.type,
+          path: pandocMetadataPath(asRawPath(filter.path, {
+            projectRoot: options.project.dir,
+            currentFileDir: dirname(options.source),
+          })),
+        };
       }
     });
 
diff --git a/src/config/types.ts b/src/config/types.ts
index 2a10678b3e..f765049fdc 100644
--- a/src/config/types.ts
+++ b/src/config/types.ts
@@ -277,11 +277,17 @@ export interface FormatDependency {
   resources?: DependencyFile[];
 }
 
-type QualifiedPath = {
+export type PathType = "project-relative" | "relative" | "absolute";
+
+type BasePath = {
   path: string;
-  type: "relative" | "project" | "absolute";
 };
 
+export type QualifiedPath = BasePath & { type: PathType };
+export type AbsolutePath = BasePath & { type: "absolute" };
+export type RelativePath = BasePath & { type: "relative" };
+export type ProjectRelativePath = BasePath & { type: "project-relative" };
+
 export interface DependencyFile {
   name: string;
   path: string;
@@ -369,10 +375,20 @@ export type QuartoFilterEntryPointQualified =
   | QuartoFilterEntryPointQualifiedFull
   | QuartoFilterSpecialEntryPoint;
 
-export type QuartoFilter = string | PandocFilter | QuartoFilterEntryPoint;
+export type QuartoFilter =
+  | string
+  | PandocFilter
+  | QuartoFilterEntryPoint
+  | QuartoFilterEntryPointQualifiedFull;
 
 export function isPandocFilter(filter: QuartoFilter): filter is PandocFilter {
-  return (<PandocFilter> filter).path !== undefined;
+  return typeof (<PandocFilter> filter).path === "string";
+}
+
+export function isQuartoFilterEntryPointQualifiedFull(
+  filter: QuartoFilter,
+): filter is QuartoFilterEntryPointQualifiedFull {
+  return typeof (<PandocFilter> filter).path !== "string";
 }
 
 export function isFilterEntryPoint(
diff --git a/src/core/qualified-path.ts b/src/core/qualified-path.ts
index f391acdad9..3a3bbb1d1e 100644
--- a/src/core/qualified-path.ts
+++ b/src/core/qualified-path.ts
@@ -6,7 +6,13 @@
  * Copyright (C) 2022 Posit Software, PBC
  */
 
-import { join, relative, resolve } from "../deno_ral/path.ts";
+import {
+  AbsolutePath,
+  ProjectRelativePath,
+  QualifiedPath,
+  RelativePath,
+} from "../config/types.ts";
+import { join } from "../deno_ral/path.ts";
 import { UnreachableError } from "./lib/error.ts";
 
 export class InvalidPathError extends Error {
@@ -20,23 +26,21 @@ export type PathInfo = {
   currentFileDir: string;
 };
 
-export type PathType = "project-relative" | "relative" | "absolute";
-
-type BasePath = {
-  value: string;
-  asAbsolute: (info?: PathInfo) => AbsolutePath;
-  asRelative: (info?: PathInfo) => RelativePath;
-  asProjectRelative: (info?: PathInfo) => ProjectRelativePath;
+export const asRawPath = (path: QualifiedPath, info: PathInfo): string => {
+  switch (path.type) {
+    case "absolute":
+      return path.path;
+    case "relative":
+      return join(info.currentFileDir, path.path);
+    case "project-relative":
+      return join(info.projectRoot, path.path);
+    default:
+      throw new UnreachableError();
+  }
 };
 
-export type QualifiedPath = BasePath & { type?: PathType };
-export type AbsolutePath = BasePath & { type: "absolute" };
-export type RelativePath = BasePath & { type: "relative" };
-export type ProjectRelativePath = BasePath & { type: "project-relative" };
-
 export function makePath(
   path: string,
-  info?: PathInfo,
   forceAbsolute?: boolean,
 ): QualifiedPath {
   const type = path.startsWith("/")
@@ -44,236 +48,23 @@ export function makePath(
     : "relative";
 
   const result: QualifiedPath = {
-    value: path,
+    path: path,
     type,
-    asAbsolute(info?: PathInfo) {
-      return toAbsolutePath(this, info);
-    },
-    asRelative(info?: PathInfo) {
-      return toRelativePath(this, info);
-    },
-    asProjectRelative(info?: PathInfo) {
-      return toProjectRelativePath(this, info);
-    },
   };
 
-  // we call asAbsolute() at least once on each path so
-  // that the path is validated; this is simply
-  // so that exceptions can be raised appropriately.
-  const quartoPaths: PathInfo = resolvePathInfo(info);
-  result.asAbsolute(quartoPaths);
-
   return result;
 }
 
-export function readTextFile(t: QualifiedPath, options?: Deno.ReadFileOptions) {
-  return Deno.readTextFile(t.asAbsolute().value, options);
-}
-
-export function readTextFileSync(
-  t: QualifiedPath,
-) {
-  return Deno.readTextFileSync(t.asAbsolute().value);
-}
-
-// validates an absolute path
-function validate(value: string, quartoPaths: PathInfo): string {
-  if (!value.startsWith(quartoPaths.projectRoot)) {
-    throw new InvalidPathError(
-      "Paths cannot resolve outside of document or project root",
-    );
-  }
-  return value;
-}
-
-function toAbsolutePath(
-  path: QualifiedPath,
-  info?: PathInfo,
-): AbsolutePath {
-  let value: string;
-
-  if (isAbsolutePath(path)) {
-    return path;
-  }
-
-  const quartoPaths: PathInfo = resolvePathInfo(info);
-
-  switch (path.type) {
-    case "project-relative":
-      // project-relative -> absolute
-      value = resolve(join(quartoPaths.projectRoot, path.value));
-      break;
-    case "relative":
-      // relative -> absolute
-      value = resolve(join(quartoPaths.currentFileDir, path.value));
-      break;
-    default:
-      if (path.value.startsWith("/")) {
-        // project-relative -> absolute
-        value = resolve(join(quartoPaths.projectRoot, path.value));
-      } else {
-        // relative -> absolute
-        value = resolve(join(quartoPaths.currentFileDir, path.value));
-      }
-  }
-  value = validate(value, quartoPaths);
-
-  return {
-    value,
-    type: "absolute",
-    asAbsolute(_info?: PathInfo) {
-      return this;
-    },
-    asRelative(info?: PathInfo) {
-      return toRelativePath(this, info);
-    },
-    asProjectRelative(info?: PathInfo) {
-      return toProjectRelativePath(this, info);
-    },
-  };
-}
-
-function toRelativePath(
-  path: QualifiedPath,
-  info?: PathInfo,
-): RelativePath {
-  let value: string;
-
-  if (isRelativePath(path)) {
-    return path;
-  }
-
-  const quartoPaths: PathInfo = resolvePathInfo(info);
-
-  switch (path.type) {
-    case "absolute":
-      // absolute -> relative
-      value = relative(quartoPaths.currentFileDir, path.value);
-      break;
-    case "project-relative": {
-      // project-relative -> absolute -> relative
-      const absPath = validate(
-        resolve(join(quartoPaths.projectRoot, path.value)),
-        quartoPaths,
-      );
-      value = relative(
-        quartoPaths.currentFileDir,
-        absPath,
-      );
-      break;
-    }
-    default:
-      if (path.value.startsWith("/")) {
-        // project-relative -> absolute -> relative
-        const absPath = validate(
-          resolve(join(quartoPaths.projectRoot, path.value)),
-          quartoPaths,
-        );
-        value = relative(
-          quartoPaths.currentFileDir,
-          absPath,
-        );
-      } else {
-        throw new UnreachableError();
-      }
-  }
-
-  return {
-    value,
-    type: "relative",
-    asAbsolute(info?: PathInfo) {
-      return toAbsolutePath(this, info);
-    },
-    asRelative(_info?: PathInfo) {
-      return this;
-    },
-    asProjectRelative(info?: PathInfo) {
-      return toProjectRelativePath(this, info);
-    },
-  };
-}
-
-function toProjectRelativePath(
-  path: QualifiedPath,
-  info?: PathInfo,
-): ProjectRelativePath {
-  let value: string;
-
-  if (isProjectRelativePath(path)) {
-    return path;
-  }
-
-  const quartoPaths: PathInfo = resolvePathInfo(info);
-
-  switch (path.type) {
-    case "absolute":
-      // absolute -> project-relative
-      value = `/${relative(quartoPaths.projectRoot, path.value)}`;
-      break;
-    case "relative":
-      // relative -> absolute -> project-relative
-      value = `/${
-        relative(
-          quartoPaths.projectRoot,
-          validate(
-            resolve(join(quartoPaths.currentFileDir, path.value)),
-            quartoPaths,
-          ),
-        )
-      }`;
-      break;
-    default:
-      if (!path.value.startsWith("/")) {
-        throw new UnreachableError();
-      } else {
-        // relative -> absolute -> project-relative
-        value = `/${
-          relative(
-            quartoPaths.projectRoot,
-            validate(
-              resolve(join(quartoPaths.currentFileDir, path.value)),
-              quartoPaths,
-            ),
-          )
-        }`;
-      }
-  }
-
-  return {
-    value,
-    type: "project-relative",
-    asAbsolute(info?: PathInfo) {
-      return toAbsolutePath(this, info);
-    },
-    asProjectRelative(_info?: PathInfo) {
-      return this;
-    },
-    asRelative(info?: PathInfo) {
-      return toRelativePath(this, info);
-    },
-  };
-}
-
-function resolvePathInfo(path?: PathInfo): PathInfo {
-  if (path !== undefined) {
-    return path;
-  }
-  throw new Error("Unimplemented");
-  // return {} as any; // FIXME this should get information from quarto's runtime.
-}
-
-function isRelativePath(path: QualifiedPath): path is RelativePath {
-  return (path.type === "relative") ||
-    (path.type === undefined && !path.value.startsWith("/"));
+export function isRelativePath(path: QualifiedPath): path is RelativePath {
+  return path.type === "relative";
 }
 
-function isProjectRelativePath(
+export function isProjectRelativePath(
   path: QualifiedPath,
 ): path is ProjectRelativePath {
-  return (path.type === "project-relative") ||
-    (path.type === undefined && path.value.startsWith("/"));
+  return path.type === "project-relative";
 }
 
-function isAbsolutePath(path: QualifiedPath): path is AbsolutePath {
+export function isAbsolutePath(path: QualifiedPath): path is AbsolutePath {
   return path.type === "absolute";
 }
diff --git a/src/extension/extension.ts b/src/extension/extension.ts
index e045c1354a..7b60ad7419 100644
--- a/src/extension/extension.ts
+++ b/src/extension/extension.ts
@@ -18,6 +18,7 @@ import {
 
 import {
   dirname,
+  extname,
   isAbsolute,
   join,
   normalize,
@@ -71,6 +72,7 @@ import { resourcePath } from "../core/resources.ts";
 import { warnOnce } from "../core/log.ts";
 import { existsSync1 } from "../core/file.ts";
 import { kFormatResources } from "../config/constants.ts";
+import { assert } from "testing/asserts";
 
 // This is where we maintain a list of extensions that have been promoted
 // to 'built-in' status. If we see these extensions, we will filter them
@@ -757,7 +759,18 @@ async function readExtension(
     });
     formatMeta.filters = (formatMeta.filters as QuartoFilter[] || []).flatMap(
       (filter) => {
-        return resolveFilter(embeddedExtensions, extensionDir, filter);
+        // that cast above is maybe invalid if filters are declared without 'type'
+        // deno-lint-ignore no-explicit-any
+        if (typeof filter === "object" && (filter as any).type === undefined) {
+          const unqualifiedPath = typeof filter.path === "string"
+            ? filter.path
+            : filter.path.path;
+          if (extname(unqualifiedPath) === ".lua") {
+            filter = { ...filter, type: "lua" };
+          }
+        }
+        const result = resolveFilter(embeddedExtensions, extensionDir, filter);
+        return result;
       },
     );
     formatMeta[kRevealJSPlugins] = (formatMeta?.[kRevealJSPlugins] as Array<
@@ -987,7 +1000,7 @@ function resolveFilter(
     // First check for the sentinel quarto filter, and allow that through
     // if it is present
     if (filter === "quarto") {
-      return filter;
+      return [filter];
     }
 
     // First attempt to load this shortcode from an embedded extension
@@ -1005,11 +1018,20 @@ function resolveFilter(
       return filters;
     } else {
       validateExtensionPath("filter", dir, filter);
-      return resolveFilterPath(dir, filter);
+      return [resolveFilterPath(dir, filter)];
     }
   } else {
-    validateExtensionPath("filter", dir, filter.path);
-    return resolveFilterPath(dir, filter);
+    if (typeof filter.path === "string") {
+      validateExtensionPath("filter", dir, filter.path);
+      return [resolveFilterPath(dir, filter)];
+    } else {
+      if (filter.path.type !== "relative") {
+        throw new Error(
+          `Failed to resolve referenced ${filter.path.path} - extensions can only declare fully-qualified paths of type "relative"`,
+        );
+      }
+      return [resolveFilterPath(dir, filter.path.path)];
+    }
   }
 }
 
@@ -1027,12 +1049,27 @@ function resolveFilterPath(
   } else {
     // deno-lint-ignore no-explicit-any
     const filterAt = ((filter as any).at) as string | undefined;
-    const result: QuartoFilter = {
-      type: filter.type,
-      path: isAbsolute(filter.path)
-        ? filter.path
-        : join(extensionDir, filter.path),
-    };
+    const result: QuartoFilter = typeof filter.path === "string"
+      ? {
+        type: filter.type,
+        at: "__quarto-auto",
+        path: {
+          type: "absolute",
+          path: isAbsolute(filter.path)
+            ? filter.path
+            : join(extensionDir, filter.path),
+        },
+      }
+      : {
+        type: filter.type,
+        at: "__quarto-auto",
+        path: {
+          type: "absolute",
+          path: isAbsolute(filter.path.path)
+            ? filter.path.path
+            : join(extensionDir, filter.path.path),
+        },
+      };
     if (filterAt === undefined) {
       return result;
     } else {