diff --git a/build.gradle.kts b/build.gradle.kts
index 8ddc45e7e8..3b5dca5ef1 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -2,7 +2,6 @@
 // Use of this source code is governed by the MIT license that can be found in the LICENSE.md file.
 import org.apache.tools.ant.taskdefs.condition.Os
 import org.aya.gradle.BuildUtil
-import java.util.*
 
 plugins {
   java
@@ -14,12 +13,15 @@ plugins {
   alias(libs.plugins.jlink) apply false
 }
 
+var projectVersion: String by rootProject.ext
 var currentPlatform: String by rootProject.ext
 var supportedPlatforms: List<String> by rootProject.ext
 var javaVersion: Int by rootProject.ext
-var deps: Properties by rootProject.ext
 
+projectVersion = libs.versions.project.get()
 javaVersion = libs.versions.java.get().toInt()
+
+// Workaround that `libs` is not available in `jacoco {}` block
 var jacocoVersion = libs.versions.jacoco.get()
 
 // Platforms we build jlink-ed aya for
@@ -33,12 +35,9 @@ supportedPlatforms = if (System.getenv("CI") == null) listOf(currentPlatform) el
   "macos-x64",
 )
 
-deps = Properties()
-file("gradle/deps.properties").reader().use(deps::load)
-
 allprojects {
   group = "org.aya-prover"
-  version = deps.getProperty("version.project")
+  version = projectVersion
 }
 
 val useJacoco = listOf("base", "pretty", "cli-impl")
diff --git a/gradle/deps.properties b/gradle/deps.properties
deleted file mode 100644
index 9b15907b85..0000000000
--- a/gradle/deps.properties
+++ /dev/null
@@ -1,6 +0,0 @@
-# Copyright (c) 2020-2023 Tesla (Yinsen) Zhang.
-# Use of this source code is governed by the MIT license that can be found in the LICENSE.md file.
-
-# Remove "-SNAPSHOT" suffix and run gradle publish to release a new version.
-# After that, increase the version number and add "-SNAPSHOT" suffix back for next cycle.
-version.project=0.30-SNAPSHOT
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index 3b7b4f6612..ccfc8fb9cd 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -1,11 +1,15 @@
 [versions]
+# The Version of this project, aka, The Aya Theorem Prover.
+# Remove "-SNAPSHOT" suffix and run gradle publish to release a new version.
+# After that, increase the version number and add "-SNAPSHOT" suffix back for next cycle.
+project = "0.30-SNAPSHOT"
+
 # Remember to update .github/workflows/{nightly-build.yml, gradle-check.yml}
 # https://openjdk.org/
 java = "20"
 # https://github.com/JetBrains/java-annotations
 annotations = "24.0.1"
 kala = "0.67.0"
-aya = "0.29.1"
 picocli = "4.7.4"
 build-util = "0.0.18"
 # https://github.com/graalvm/native-build-tools
@@ -31,7 +35,6 @@ jlink = { id = "org.beryx.jlink", version.ref = "jlink" }
 [libraries]
 annotations = { group = "org.jetbrains", name = "annotations", version.ref = "annotations" }
 
-aya-tools = { group = "org.aya-prover", name = "tools", version.ref = "aya" }
 aya-ij-core = { group = "org.aya-prover.upstream", name = "ij-parsing-core", version.ref = "build-util" }
 aya-ij-text = { group = "org.aya-prover.upstream", name = "ij-util-text", version.ref = "build-util" }
 aya-ij-wrapper = { group = "org.aya-prover.upstream", name = "ij-parsing-wrapper", version.ref = "build-util" }