chore: task upgrade — bump deps + fix kotlin_android + python pyproject

`task upgrade` ran end-to-end. Two issues surfaced and were patched in
the run:

- `crates/html-to-markdown-py/src/pyproject.toml` pointed maturin at
  `../../crates/html-to-markdown-py/Cargo.toml` (which resolves to
  `crates/crates/…` from the pyproject's own directory). Corrected to
  `../Cargo.toml`. `uv sync --all-packages --all-extras --upgrade`
  now completes; this had been broken silently — the publish workflow
  builds via `maturin build` with explicit paths, so the bug only fired
  on local `uv sync` / `task upgrade`.

- `com.github.ben-manes.versions` plugin (0.52.0 / latest 0.53.0)
  throws `java.util.ConcurrentModificationException` under Gradle 9.5.1
  on every `:dependencyUpdates` invocation. The plugin has not shipped
  since 2024-11. Both `alef update --latest` and `task kotlin_android:upgrade`
  consequently failed the rest of the upgrade chain. Inert-echo the probe
  in both alef.toml (`[crates.update.kotlin_android]`) and
  `.task/languages/kotlin_android.yml` until upstream lands a Gradle 9
  fix or we swap to `nl.littlerobots.version-catalog-update`.

Remaining diffs are the upgrade-chain outputs: gau-driven GitHub Actions
pins, Cargo workspace deps, pnpm/uv/composer/Gemfile lockfile bumps,
alef docs regen triggered by the version sync, and per-language README
re-renders.

Author: Goldziher

.github/workflows/ci-e2e.yaml

@@ -1016,7 +1016,7 @@ jobs:
         uses: actions/checkout@v6.0.2
 
       - name: Setup Elixir
-        uses: erlef/setup-beam@v1.24.0
+        uses: erlef/setup-beam@v1.24
         with:
           elixir-version: "1.19"
           otp-version: "28.1"

.task/languages/kotlin_android.yml

@@ -1,19 +1,22 @@
 version: "3"
 internal: true
 
+# `com.github.ben-manes.versions` (pin 0.52.0, latest 0.53.0) throws
+# `java.util.ConcurrentModificationException` under Gradle 9.5.1 on every
+# `:dependencyUpdates` invocation; the plugin has not shipped a release
+# since 2024-11. Until upstream fixes it (or we swap to
+# `nl.littlerobots.version-catalog-update`), the kotlin_android update/upgrade
+# probe is a no-op so `task upgrade` does not fail on the rest of the chain.
+# Mirror the rationale in alef.toml `[crates.update.kotlin_android]`.
 tasks:
   update:
-    desc: "Update Kotlin/Android dependencies within major versions (gradlew dependencyUpdates)"
+    desc: "Update Kotlin/Android dependencies (skipped: ben-manes versions plugin incompatible with Gradle 9.x)"
     silent: false
     cmds:
-      - cmd: |
-          cd packages/kotlin-android && ./gradlew dependencyUpdates
-        ignore_error: false
+      - 'echo "[kotlin_android] skip: ben-manes/gradle-versions-plugin incompatible with Gradle 9.x"'
 
   upgrade:
-    desc: "Report Kotlin/Android dependency upgrades (gradlew dependencyUpdates — Android SDK / AGP bumps need manual review for binary-compat impact)"
+    desc: "Report Kotlin/Android dependency upgrades (skipped: ben-manes versions plugin incompatible with Gradle 9.x)"
     silent: false
     cmds:
-      - cmd: |
-          cd packages/kotlin-android && ./gradlew dependencyUpdates
-        ignore_error: false
+      - 'echo "[kotlin_android] skip: ben-manes/gradle-versions-plugin incompatible with Gradle 9.x"'

Cargo.toml

@@ -43,7 +43,7 @@ clap = { version = "4.6", features = ["derive"] }
 clap_complete = "4.6"
 clap_mangen = "0.3"
 encoding_rs = "0.8"
-ext-php-rs = "0.15.13"
+ext-php-rs = "0.15.14"
 html-to-markdown-rs = { version = "3.5.0", path = "crates/html-to-markdown" }
 html5ever = "0.39.0"
 once_cell = "1.21"

alef.toml

@@ -311,6 +311,18 @@ precondition = "command -v gradle >/dev/null 2>&1"
 format = "cd packages/kotlin-android && gradle ktlintFormat --no-daemon"
 check = "cd packages/kotlin-android && gradle ktlintCheck --no-daemon"
 
+[crates.update.kotlin_android]
+# The com.github.ben-manes.versions plugin (current pin 0.52.0, latest 0.53.0)
+# throws `java.util.ConcurrentModificationException` under Gradle 9.5.1 on every
+# `:dependencyUpdates` invocation. The plugin has not shipped a release since
+# 2024-11 and the incompatibility is unpatched upstream. `task upgrade` and
+# `alef update --latest` both consequently fail on the kotlin_android step.
+# Skip the probe with an inert echo until either the plugin ships a Gradle 9
+# fix or we swap to `nl.littlerobots.version-catalog-update`.
+precondition = "command -v gradle >/dev/null 2>&1"
+update = "echo '[kotlin_android] skip: ben-manes/gradle-versions-plugin incompatible with Gradle 9.x'"
+upgrade = "echo '[kotlin_android] skip: ben-manes/gradle-versions-plugin incompatible with Gradle 9.x'"
+
 [crates.lint.swift]
 precondition = "command -v swift >/dev/null 2>&1"
 format = "swift format --in-place --recursive packages/swift/Sources"