Fix upgrade-packs.sh to actually refresh pack lock files

Previously, codeql pack upgrade was a no-op for packs with pinned
codeql/<lang>-all dependencies because the existing pin already
satisfied the constraint. This left codeql-pack.lock.yml files
unchanged across CLI bumps, even though newer compatible library
pack versions were available.

The fix temporarily rewrites the pinned dependency to a wildcard
before running codeql pack upgrade, then restores the manifest and
pins it to the version resolved into the lock file.

Also regenerates all pack lock files and re-pins manifests against
CodeQL CLI v2.25.3, and refreshes ruby/rust/swift PrintAST/PrintCFG
.expected files for benign output ordering and library behavior
changes introduced by the upgraded codeql/*-all packs.

Author: data-douser

server/ql/actions/tools/src/codeql-pack.lock.yml

@@ -2,31 +2,31 @@
 lockVersion: 1.0.0
 dependencies:
   codeql/actions-all:
-    version: 0.4.32
+    version: 0.4.34
   codeql/concepts:
-    version: 0.0.20
+    version: 0.0.22
   codeql/controlflow:
-    version: 2.0.30
+    version: 2.0.32
   codeql/dataflow:
-    version: 2.1.2
+    version: 2.1.4
   codeql/javascript-all:
-    version: 2.6.26
+    version: 2.6.28
   codeql/mad:
-    version: 1.0.46
+    version: 1.0.48
   codeql/regex:
-    version: 1.0.46
+    version: 1.0.48
   codeql/ssa:
-    version: 2.0.22
+    version: 2.0.24
   codeql/threat-models:
-    version: 1.0.46
+    version: 1.0.48
   codeql/tutorial:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typetracking:
-    version: 2.0.30
+    version: 2.0.32
   codeql/util:
-    version: 2.0.33
+    version: 2.0.35
   codeql/xml:
-    version: 1.0.46
+    version: 1.0.48
   codeql/yaml:
-    version: 1.0.46
+    version: 1.0.48
 compiled: false

server/ql/actions/tools/src/codeql-pack.yml

@@ -3,4 +3,4 @@ version: 2.25.3
 description: 'Queries for codeql-development-mcp-server tools for actions language'
 library: false
 dependencies:
-  codeql/actions-all: 0.4.32
+  codeql/actions-all: 0.4.34

server/ql/actions/tools/test/codeql-pack.lock.yml

@@ -2,31 +2,31 @@
 lockVersion: 1.0.0
 dependencies:
   codeql/actions-all:
-    version: 0.4.32
+    version: 0.4.34
   codeql/concepts:
-    version: 0.0.20
+    version: 0.0.22
   codeql/controlflow:
-    version: 2.0.30
+    version: 2.0.32
   codeql/dataflow:
-    version: 2.1.2
+    version: 2.1.4
   codeql/javascript-all:
-    version: 2.6.26
+    version: 2.6.28
   codeql/mad:
-    version: 1.0.46
+    version: 1.0.48
   codeql/regex:
-    version: 1.0.46
+    version: 1.0.48
   codeql/ssa:
-    version: 2.0.22
+    version: 2.0.24
   codeql/threat-models:
-    version: 1.0.46
+    version: 1.0.48
   codeql/tutorial:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typetracking:
-    version: 2.0.30
+    version: 2.0.32
   codeql/util:
-    version: 2.0.33
+    version: 2.0.35
   codeql/xml:
-    version: 1.0.46
+    version: 1.0.48
   codeql/yaml:
-    version: 1.0.46
+    version: 1.0.48
 compiled: false

server/ql/cpp/tools/src/codeql-pack.lock.yml

@@ -2,27 +2,27 @@
 lockVersion: 1.0.0
 dependencies:
   codeql/controlflow:
-    version: 2.0.30
+    version: 2.0.32
   codeql/cpp-all:
-    version: 8.0.3
+    version: 10.0.0
   codeql/dataflow:
-    version: 2.1.2
+    version: 2.1.4
   codeql/mad:
-    version: 1.0.46
+    version: 1.0.48
   codeql/quantum:
-    version: 0.0.24
+    version: 0.0.26
   codeql/rangeanalysis:
-    version: 1.0.46
+    version: 1.0.48
   codeql/ssa:
-    version: 2.0.22
+    version: 2.0.24
   codeql/tutorial:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typeflow:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typetracking:
-    version: 2.0.30
+    version: 2.0.32
   codeql/util:
-    version: 2.0.33
+    version: 2.0.35
   codeql/xml:
-    version: 1.0.46
+    version: 1.0.48
 compiled: false

server/ql/cpp/tools/src/codeql-pack.yml

@@ -3,4 +3,4 @@ version: 2.25.3
 description: 'Queries for codeql-development-mcp-server tools for cpp language'
 library: false
 dependencies:
-  codeql/cpp-all: 8.0.3
+  codeql/cpp-all: 10.0.0

server/ql/cpp/tools/test/codeql-pack.lock.yml

@@ -2,27 +2,27 @@
 lockVersion: 1.0.0
 dependencies:
   codeql/controlflow:
-    version: 2.0.30
+    version: 2.0.32
   codeql/cpp-all:
-    version: 8.0.3
+    version: 10.0.0
   codeql/dataflow:
-    version: 2.1.2
+    version: 2.1.4
   codeql/mad:
-    version: 1.0.46
+    version: 1.0.48
   codeql/quantum:
-    version: 0.0.24
+    version: 0.0.26
   codeql/rangeanalysis:
-    version: 1.0.46
+    version: 1.0.48
   codeql/ssa:
-    version: 2.0.22
+    version: 2.0.24
   codeql/tutorial:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typeflow:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typetracking:
-    version: 2.0.30
+    version: 2.0.32
   codeql/util:
-    version: 2.0.33
+    version: 2.0.35
   codeql/xml:
-    version: 1.0.46
+    version: 1.0.48
 compiled: false

server/ql/csharp/tools/src/codeql-pack.lock.yml

@@ -2,23 +2,23 @@
 lockVersion: 1.0.0
 dependencies:
   codeql/controlflow:
-    version: 2.0.30
+    version: 2.0.32
   codeql/csharp-all:
-    version: 5.4.11
+    version: 5.5.0
   codeql/dataflow:
-    version: 2.1.2
+    version: 2.1.4
   codeql/mad:
-    version: 1.0.46
+    version: 1.0.48
   codeql/ssa:
-    version: 2.0.22
+    version: 2.0.24
   codeql/threat-models:
-    version: 1.0.46
+    version: 1.0.48
   codeql/tutorial:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typetracking:
-    version: 2.0.30
+    version: 2.0.32
   codeql/util:
-    version: 2.0.33
+    version: 2.0.35
   codeql/xml:
-    version: 1.0.46
+    version: 1.0.48
 compiled: false

server/ql/csharp/tools/src/codeql-pack.yml

@@ -3,4 +3,4 @@ version: 2.25.3
 description: 'Queries for codeql-development-mcp-server tools for csharp language'
 library: false
 dependencies:
-  codeql/csharp-all: 5.4.11
+  codeql/csharp-all: 5.5.0

server/ql/csharp/tools/test/codeql-pack.lock.yml

@@ -2,23 +2,23 @@
 lockVersion: 1.0.0
 dependencies:
   codeql/controlflow:
-    version: 2.0.30
+    version: 2.0.32
   codeql/csharp-all:
-    version: 5.4.11
+    version: 5.5.0
   codeql/dataflow:
-    version: 2.1.2
+    version: 2.1.4
   codeql/mad:
-    version: 1.0.46
+    version: 1.0.48
   codeql/ssa:
-    version: 2.0.22
+    version: 2.0.24
   codeql/threat-models:
-    version: 1.0.46
+    version: 1.0.48
   codeql/tutorial:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typetracking:
-    version: 2.0.30
+    version: 2.0.32
   codeql/util:
-    version: 2.0.33
+    version: 2.0.35
   codeql/xml:
-    version: 1.0.46
+    version: 1.0.48
 compiled: false

server/ql/go/tools/src/codeql-pack.lock.yml

@@ -2,23 +2,23 @@
 lockVersion: 1.0.0
 dependencies:
   codeql/concepts:
-    version: 0.0.20
+    version: 0.0.22
   codeql/controlflow:
-    version: 2.0.30
+    version: 2.0.32
   codeql/dataflow:
-    version: 2.1.2
+    version: 2.1.4
   codeql/go-all:
-    version: 7.0.4
+    version: 7.0.6
   codeql/mad:
-    version: 1.0.46
+    version: 1.0.48
   codeql/ssa:
-    version: 2.0.22
+    version: 2.0.24
   codeql/threat-models:
-    version: 1.0.46
+    version: 1.0.48
   codeql/tutorial:
-    version: 1.0.46
+    version: 1.0.48
   codeql/typetracking:
-    version: 2.0.30
+    version: 2.0.32
   codeql/util:
-    version: 2.0.33
+    version: 2.0.35
 compiled: false