Adjust for base paths possibly being non-normalized

Fixes test failures with JuliaLang/julia#60251.
Also fixes an unrelated test where Revise was using the wrong PkgId
for Core.Compiler (failure not seen on CI, because it's explicitly
disabled there).

Author: Keno

src/pkgs.jl

@@ -362,7 +362,7 @@ function has_writable_paths(pkgdata::PkgData)
 end
 
 function watch_includes(mod::Module, fn::AbstractString)
-    @lock included_files_lock push!(included_files, (mod, normpath(abspath(fn))))
+    @lock included_files_lock push!(included_files, (mod, realpath(fn)))
 end
 
 ## Working with Pkg and code-loading
@@ -390,6 +390,7 @@ function manifest_paths!(pkgpaths::Dict, manifest_file::String)
         for entry in entries
             id = PkgId(UUID(entry["uuid"]::String), name)
             path = Base.explicit_manifest_entry_path(manifest_file, id, entry)
+            ispath(path) && (path = realpath(path))
             if path isa String
                 if isfile(path)
                     # Workaround for #802
@@ -423,7 +424,7 @@ function watch_manifest(mfile::String)
                 for (id, pkgdir) in pkgdirs
                     if haskey(pkgdatas, id)
                         pkgdata = pkgdatas[id]
-                        if pkgdir != basedir(pkgdata)
+                        if !samefile(pkgdir, basedir(pkgdata))
                             ## The package directory has changed
                             @debug "Pkg" _group="pathswitch" oldpath=basedir(pkgdata) newpath=pkgdir
                             push!(pathreplacements, basedir(pkgdata)=>pkgdir)
@@ -434,7 +435,7 @@ function watch_manifest(mfile::String)
                 # Update the paths in the watchlist
                 for (oldpath, newpath) in pathreplacements
                     for (_, pkgdata) in pkgdatas
-                        if basedir(pkgdata) == oldpath
+                        if samefile(basedir(pkgdata), oldpath)
                             switch_basepath(pkgdata, newpath)
                         end
                     end

src/recipes.jl

@@ -9,15 +9,15 @@ detected during tracking are applied immediately. Optionally, if `revise_throw`
 `true`, `revise()` will throw if any exceptions are encountered while revising.
 """
 function track(mod::Module; modified_files=revision_queue, revise_throw::Bool=!isinteractive())
-    id = Base.moduleroot(mod) == Core.Compiler ?
-        PkgId(mod, "Core.Compiler") :
-        PkgId(mod)
+    id = pkgidid_for_mod(mod)
     modname = nameof(mod)
     ret = _track(id, modname; modified_files=modified_files)
     revise(; throw=revise_throw) # force revision so following calls in the same block work
     return ret
 end
 
+pkgidid_for_mod(mod) = id = Base.moduleroot(mod) == Core.Compiler ? PkgId(mod, "Core.Compiler") : PkgId(mod)
+
 const vstring = "v$(VERSION.major).$(VERSION.minor)"
 
 function inpath(path::AbstractString, dirs::Vector{String})
@@ -140,7 +140,7 @@ function track_subdir_from_git!(pkgdata::PkgData, subdir::AbstractString; commit
     if repo == nothing
         throw(GitRepoException(subdir))
     end
-    prefix = string(relpath(subdir, repo_path), "/")   # git-relative path of this subdir
+    prefix = string(relpath(realpath(subdir), realpath(repo_path)), "/")   # git-relative path of this subdir
     tree = git_tree(repo, commit)
     files = Iterators.filter(file->startswith(file, prefix) && endswith(file, ".jl"), keys(tree))
     ccall((:giterr_clear, :libgit2), Cvoid, ())  # necessary to avoid errors like "the global/xdg file 'attributes' doesn't exist: No such file or directory"

test/runtests.jl

@@ -499,8 +499,10 @@ const issue639report = []
                 @test Revise.RelocatableExpr(definition(m)) != rex
                 # CodeTracking methods
                 m3 = first(methods(eval(fn3)))
-                m3file = joinpath(dn, "subdir", "file3.jl")
-                @test whereis(m3) == (m3file, 1)
+                m3file = realpath(joinpath(dn, "subdir", "file3.jl"))
+                w = whereis(m3)
+                @test samefile(w[1], m3file)
+                @test w[2] == 1
                 @test signatures_at(m3file, 1) == [Revise.SigInfo(nothing, m3.sig)]
                 @test signatures_at(eval(Symbol(modname)), joinpath("src", "subdir", "file3.jl"), 1) == [Revise.SigInfo(nothing, m3.sig)]
 
@@ -2990,7 +2992,7 @@ const issue639report = []
             if repo != nothing && isfile(joinpath(path, "VERSION")) && isdir(joinpath(path, "base"))
                 # Tracking Core.Compiler
                 Revise.track(Core.Compiler)
-                id = Base.PkgId(Core.Compiler)
+                id = Revise.pkgidid_for_mod(Core.Compiler)
                 pkgdata = Revise.pkgdatas[id]
                 @test any(k->endswith(k, "optimize.jl"), Revise.srcfiles(pkgdata))
                 m = first(methods(Core.Compiler.typeinf_code))