Migrate from yarn to pnpm (#12529)

* migrate yarn to pnpm

* chore: update pnpm version to 10.33.0 across all package.json files

* chore: update .npmrc and package.json for improved dependency management

* chore: unify Clojure, Node, and Java version in workflow files

* fix: enable shamefully-hoist for now and add electron, keytar to onlyBuiltDependencies

* feat: add cider/piggieback dependency and update nREPL middleware configuration to silence warnings

* ensure pnpm setup prior to node setup

* fix: update logseq/bb-tasks git SHA

* feat: add pnpm configuration for onlyBuiltDependencies in package.json

* feat: add onlyBuiltDependencies configuration for better-sqlite3 in pnpm settings

* chore: update pnpm lockfile

* fix: resolve merge conflicts

* fix: remove invisible characters from markdown headers

* fix: update .npmrc comments for clarity on lockfile usage

* Revert "feat: add cider/piggieback dependency and update nREPL middleware configuration to silence warnings"

This reverts commit 70a111936f.

* fix: remove invisible characters from various README files and add .editorconfig

* fix: clarify lockfile resolution process in SKILL.md

---------

Co-authored-by: Tienson Qin <tiensonqin@gmail.com>

.github/workflows/deps-graph-parser.yml

@@ -42,12 +42,17 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Set up pnpm
+        uses: pnpm/action-setup@v4
+        with:
+          version: 10.33.0
+
       - name: Set up Node
         uses: actions/setup-node@v4
         with:
           node-version: ${{ env.NODE_VERSION }}
-          cache: 'yarn'
-          cache-dependency-path: deps/graph-parser/yarn.lock
+          cache: 'pnpm'
+          cache-dependency-path: deps/graph-parser/pnpm-lock.yaml
 
       - name: Set up Java
         uses: actions/setup-java@v4
@@ -75,14 +80,14 @@ jobs:
         if: steps.clojure-deps.outputs.cache-hit != 'true'
         run: clojure -A:test -P
 
-      - name: Fetch yarn deps
-        run: yarn install --frozen-lockfile
+      - name: Fetch pnpm deps
+        run: pnpm install --frozen-lockfile
 
       - name: Run ClojureScript tests
         run: clojure -M:test
 
       - name: Run nbb-logseq tests
-        run: yarn test
+        run: pnpm test
 
       # In this job because it depends on an npm package
       - name: Load namespaces into nbb-logseq