Update manifest entry of project for non-local manifests

[quinnj]

Instead of just skipping manifest pruning all together (which is tricky because we're often not operating in a root-level context which would correctly prune everything), we can at least update the dependency list of the currently activated project in the root-level manifest.

[quinnj]

Will try to think of a way to add a test here

[nickrobinson251]

thanks for fixing this!

The problem we're seeing is that, if you have a package Foo with a Project.toml (at e.g. packages/Foo/Project.toml) which looks like:

name = "Foo"
uuid = "801270c1-6d38-4c07-85b6-74a2f576d89a"
manifest = "../../Manifest.toml"
version = "0.1.0"

[deps]
Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
ContextVariablesX = "6add18c4-b38d-439d-96f6-d6bc489c04c5"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
ExceptionUnwrapping = "460bff9d-24e4-43bc-9d9f-a8973cb893f4"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"

[compat]
ReTestItems = "1"

[extras]
DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
ReTestItems = "817f1d60-ba6b-4fd5-9520-3cf149f6a823"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["DeepDiffs", "JSON3", "ReTestItems", "Test"]

note the manifest = "../../Manifest.toml" entry

And then you add and then remove a package

] activate Foo
] add Example
] rm Example

which should leave the Project.toml (packages/Foo/Project.toml) and Manifest.toml (../../Manifest.toml) without any changes

But we see

(Foo) pkg> add Example
   Resolving package versions...
    Updating `~/packages/Foo/Project.toml`
  [7876af07] + Example v0.5.3
    Updating `~/Manifest.toml`
  [7876af07] + Example v0.5.3

(Foo) pkg> rm Example
    Updating `~/packages/Foo/Project.toml`
  [7876af07] - Example v0.5.3
  No Changes to `~/Manifest.toml`

And the Manifest.toml is left with a diff like:

diff --git a/Manifest.toml b/Manifest.toml
index 1311df8842..2042e8dd9d 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.9.2"
 manifest_format = "2.0"
-project_hash = "53c4ec67dcb0841eab26478fa1ef6c1836f9ee8b"
+project_hash = "c42550b13eba1529c8ab6377082cae8993859c62"
 
 [[deps.ANSIColoredPrinters]]
 git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
@@ -497,6 +497,11 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237"
 uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
 version = "1.0.4"
 
+[[deps.Example]]
+git-tree-sha1 = "46e44e869b4d90b96bd8ed1fdcf32244fddfb6cc"
+uuid = "7876af07-990d-54b4-ab0e-23690620f79a"
+version = "0.5.3"
+
 [[deps.ExceptionUnwrapping]]
 deps = ["Test"]
 git-tree-sha1 = "e90caa41f5a86296e014e148ee061bd6c3edec96"
@@ -1632,7 +1637,7 @@ uuid = "66d59315-31dc-41c8-b200-e39bcbf712f1"
 version = "0.1.0"
 
 [[deps.Foo]]
-deps = ["Compat", "ContextVariablesX", "Dates", "ExceptionUnwrapping", "JSON", "Logging"]
+deps = ["Compat", "ContextVariablesX", "Dates", "Example", "ExceptionUnwrapping", "JSON", "Logging"]
 path = "packages/Foo"
 uuid = "801270c1-6d38-4c07-85b6-74a2f576d89a"
 version = "0.1.0"

Which has two issues:

1. The deps.Foo entry is left with Example in its deps
2. There is a deps.Example entry, even though nothing depends on Example (given that Foo doesn't depend on Example after the rm)

This PR is to at least fix the first of those issues (cleaning up deps.Foo)

[nickrobinson251]

Can we add backport 1.9 to this?

[nickrobinson251]

LGTM!

Opened an issue for the second part of this #3590