lein repl and any command with "lein" Doesn't Work

Question

I have just started learning Clojure from Daniel Higginbottam's book called Clojure for the Brave and True. Needless to say, you need Leiningen and Cider for a good Clojure workflow.

Before I have tried installing cider to emacs, my Leiningen was working fine but somehow after I have tingled some settings with emacs (installing cider), my Leiningen installation started to give stack trace errors such as below: (I don't know how can this happen at all)

How can I fix this?

(Also, I have tried re-installing Leiningen, which didn't solve the issue.)

Java HotSpot(TM) 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
clojure.lang.Compiler$CompilerException: Syntax error compiling at (cider/nrepl.clj:1:1).
#:clojure.error{:phase :compile-syntax-check, :line 1, :column 1, :source "cider/nrepl.clj"}
 at clojure.lang.Compiler.load (Compiler.java:7648)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:459)
    clojure.lang.RT.load (RT.java:424)
    clojure.core$load$fn__6839.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6780.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:421)
    cider_nrepl.plugin$eval659$loading__6721__auto____660.invoke (plugin.clj:1)
    cider_nrepl.plugin$eval659.invokeStatic (plugin.clj:1)
    cider_nrepl.plugin$eval659.invoke (plugin.clj:1)
    clojure.lang.Compiler.eval (Compiler.java:7177)
    clojure.lang.Compiler.eval (Compiler.java:7166)
    clojure.lang.Compiler.load (Compiler.java:7636)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:459)
    clojure.lang.RT.load (RT.java:424)
    clojure.core$load$fn__6839.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6780.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    leiningen.core.utils$require_resolve.invokeStatic (utils.clj:102)
    leiningen.core.utils$require_resolve.invoke (utils.clj:95)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:850)
    leiningen.core.project$apply_middleware.invoke (project.clj:843)
    clojure.lang.ArrayChunk.reduce (ArrayChunk.java:58)
    clojure.core.protocols$fn__8154.invokeStatic (protocols.clj:136)
    clojure.core.protocols/fn (protocols.clj:124)
    clojure.core.protocols$fn__8114$G__8109__8123.invoke (protocols.clj:19)
    clojure.core.protocols$seq_reduce.invokeStatic (protocols.clj:31)
    clojure.core.protocols$fn__8146.invokeStatic (protocols.clj:75)
    clojure.core.protocols/fn (protocols.clj:75)
    clojure.core.protocols$fn__8088$G__8083__8101.invoke (protocols.clj:13)
    clojure.core$reduce.invokeStatic (core.clj:6828)
    clojure.core$reduce.invoke (core.clj:6810)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:845)
    leiningen.core.project$apply_middleware.invoke (project.clj:843)
    leiningen.core.project$activate_middleware.invokeStatic (project.clj:877)
    leiningen.core.project$activate_middleware.invoke (project.clj:873)
    leiningen.core.project$set_profiles.invokeStatic (project.clj:966)
    leiningen.core.project$set_profiles.doInvoke (project.clj:959)
    clojure.lang.RestFn.invoke (RestFn.java:425)
    leiningen.core.project$init_project.invokeStatic (project.clj:1041)
    leiningen.core.project$init_project.invoke (project.clj:1016)
    leiningen.core.project$init_project.invokeStatic (project.clj:1042)
    leiningen.core.project$init_project.invoke (project.clj:1016)
    leiningen.core.main$default_project.invokeStatic (main.clj:419)
    leiningen.core.main$default_project.invoke (main.clj:412)
    leiningen.core.main$_main$fn__7419.invoke (main.clj:449)
    leiningen.core.main$_main.invokeStatic (main.clj:442)
    leiningen.core.main$_main.doInvoke (main.clj:439)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.core$apply.invokeStatic (core.clj:665)
    clojure.main$main_opt.invokeStatic (main.clj:514)
    clojure.main$main_opt.invoke (main.clj:510)
    clojure.main$main.invokeStatic (main.clj:664)
    clojure.main$main.doInvoke (main.clj:616)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.main.main (main.java:40)
Caused by: java.io.FileNotFoundException: Could not locate clojure/tools/nrepl/server__init.class, clojure/tools/nrepl/server.clj or clojure/tools/nrepl/server.cljc on classpath.
 at clojure.lang.RT.load (RT.java:462)
    clojure.lang.RT.load (RT.java:424)
    clojure.core$load$fn__6839.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6780.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:1289)
    cider.nrepl$eval665$loading__6721__auto____666.invoke (nrepl.clj:1)
    cider.nrepl$eval665.invokeStatic (nrepl.clj:1)
    cider.nrepl$eval665.invoke (nrepl.clj:1)
    clojure.lang.Compiler.eval (Compiler.java:7177)
    clojure.lang.Compiler.eval (Compiler.java:7166)
    clojure.lang.Compiler.load (Compiler.java:7636)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:459)
    clojure.lang.RT.load (RT.java:424)
    clojure.core$load$fn__6839.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6780.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:421)
    cider_nrepl.plugin$eval659$loading__6721__auto____660.invoke (plugin.clj:1)
    cider_nrepl.plugin$eval659.invokeStatic (plugin.clj:1)
    cider_nrepl.plugin$eval659.invoke (plugin.clj:1)
    clojure.lang.Compiler.eval (Compiler.java:7177)
    clojure.lang.Compiler.eval (Compiler.java:7166)
    clojure.lang.Compiler.load (Compiler.java:7636)
    clojure.lang.RT.loadResourceScript (RT.java:381)
    clojure.lang.RT.loadResourceScript (RT.java:372)
    clojure.lang.RT.load (RT.java:459)
    clojure.lang.RT.load (RT.java:424)
    clojure.core$load$fn__6839.invoke (core.clj:6126)
    clojure.core$load.invokeStatic (core.clj:6125)
    clojure.core$load.doInvoke (core.clj:6109)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    clojure.core$load_one.invokeStatic (core.clj:5908)
    clojure.core$load_one.invoke (core.clj:5903)
    clojure.core$load_lib$fn__6780.invoke (core.clj:5948)
    clojure.core$load_lib.invokeStatic (core.clj:5947)
    clojure.core$load_lib.doInvoke (core.clj:5928)
    clojure.lang.RestFn.applyTo (RestFn.java:142)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$load_libs.invokeStatic (core.clj:5985)
    clojure.core$load_libs.doInvoke (core.clj:5969)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.core$apply.invokeStatic (core.clj:667)
    clojure.core$require.invokeStatic (core.clj:6007)
    clojure.core$require.doInvoke (core.clj:6007)
    clojure.lang.RestFn.invoke (RestFn.java:408)
    leiningen.core.utils$require_resolve.invokeStatic (utils.clj:102)
    leiningen.core.utils$require_resolve.invoke (utils.clj:95)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:850)
    leiningen.core.project$apply_middleware.invoke (project.clj:843)
    clojure.lang.ArrayChunk.reduce (ArrayChunk.java:58)
    clojure.core.protocols$fn__8154.invokeStatic (protocols.clj:136)
    clojure.core.protocols/fn (protocols.clj:124)
    clojure.core.protocols$fn__8114$G__8109__8123.invoke (protocols.clj:19)
    clojure.core.protocols$seq_reduce.invokeStatic (protocols.clj:31)
    clojure.core.protocols$fn__8146.invokeStatic (protocols.clj:75)
    clojure.core.protocols/fn (protocols.clj:75)
    clojure.core.protocols$fn__8088$G__8083__8101.invoke (protocols.clj:13)
    clojure.core$reduce.invokeStatic (core.clj:6828)
    clojure.core$reduce.invoke (core.clj:6810)
    leiningen.core.project$apply_middleware.invokeStatic (project.clj:845)
    leiningen.core.project$apply_middleware.invoke (project.clj:843)
    leiningen.core.project$activate_middleware.invokeStatic (project.clj:877)
    leiningen.core.project$activate_middleware.invoke (project.clj:873)
    leiningen.core.project$set_profiles.invokeStatic (project.clj:966)
    leiningen.core.project$set_profiles.doInvoke (project.clj:959)
    clojure.lang.RestFn.invoke (RestFn.java:425)
    leiningen.core.project$init_project.invokeStatic (project.clj:1041)
    leiningen.core.project$init_project.invoke (project.clj:1016)
    leiningen.core.project$init_project.invokeStatic (project.clj:1042)
    leiningen.core.project$init_project.invoke (project.clj:1016)
    leiningen.core.main$default_project.invokeStatic (main.clj:419)
    leiningen.core.main$default_project.invoke (main.clj:412)
    leiningen.core.main$_main$fn__7419.invoke (main.clj:449)
    leiningen.core.main$_main.invokeStatic (main.clj:442)
    leiningen.core.main$_main.doInvoke (main.clj:439)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.core$apply.invokeStatic (core.clj:665)
    clojure.main$main_opt.invokeStatic (main.clj:514)
    clojure.main$main_opt.invoke (main.clj:510)
    clojure.main$main.invokeStatic (main.clj:664)
    clojure.main$main.doInvoke (main.clj:616)
    clojure.lang.RestFn.applyTo (RestFn.java:137)
    clojure.lang.Var.applyTo (Var.java:705)
    clojure.main.main (main.java:40)