diff --git a/infra/base-images/base-builder/indexer/manifest_types.py b/infra/base-images/base-builder/indexer/manifest_types.py
index 0013afb2caa3..bb4239c695be 100644
--- a/infra/base-images/base-builder/indexer/manifest_types.py
+++ b/infra/base-images/base-builder/indexer/manifest_types.py
@@ -90,7 +90,7 @@ class SourceRef:
   @classmethod
   def from_dict(cls, data: dict[str, Any]) -> Self:
     """Creates a SourceRef object from a deserialized dict."""
-    return SourceRef(  # pyrefly: ignore[bad-return]
+    return cls(
         url=data["url"], rev=data["rev"], type=RepositoryType(data["type"])
     )
 
@@ -108,7 +108,7 @@ class Reproducibility:
   @classmethod
   def from_dict(cls, data: dict[str, Any]) -> Self:
     """Creates a Reproducibility object from a deserialized dict."""
-    return Reproducibility(  # pyrefly: ignore[bad-return]
+    return cls(
         success_count=data["success_count"],
         trial_count=data["trial_count"],
     )
@@ -210,7 +210,7 @@ def from_dict(cls, config_dict: Mapping[str, Any]) -> Self:
     harness_kind = HarnessKind(
         config_dict.get("harness_kind", HarnessKind.BINARY)
     )
-    return CommandLineBinaryConfig(  # pyrefly: ignore[bad-return]
+    return cls(
         kind=kind,
         harness_kind=harness_kind,
         binary_name=config_dict["binary_name"],
@@ -319,7 +319,7 @@ def from_dict(cls, data: dict[str, Any]) -> Self:
       logging.warning(
           "Unsupported manifest version %s detected. Not upgrading.", version
       )
-    return Manifest(  # pyrefly: ignore[bad-return]
+    return cls(
         version=version,
         index_db_version=data.get("index_db_version"),
         name=data["name"],
diff --git a/projects/argo/project.yaml b/projects/argo/project.yaml
index 0c60dc373911..37bae11e92ba 100644
--- a/projects/argo/project.yaml
+++ b/projects/argo/project.yaml
@@ -1,6 +1,6 @@
 base_os_version: ubuntu-24-04
 homepage: "https://argoproj.github.io/"
-main_repo: "https://github.com/argoproj"
+main_repo: "https://github.com/argoproj/argo-cd"
 primary_contact: "terrytangyuan@gmail.com"
 auto_ccs :
   - "adam@adalogics.com"
diff --git a/projects/bignum-fuzzer/project.yaml b/projects/bignum-fuzzer/project.yaml
index 6c88bc1011ab..d46dcddb3306 100644
--- a/projects/bignum-fuzzer/project.yaml
+++ b/projects/bignum-fuzzer/project.yaml
@@ -15,7 +15,7 @@ auto_ccs:
     - "mbed-tls-security@lists.trustedfirmware.org"
     - "libmpdec4@gmail.com"
     - "richard@levitte.org"
-main_repo: 'https://github.com/guidovranken/bignum-fuzzer'
+main_repo: "https://github.com/sjamaan/bignum-fuzzer"
 fuzzing_engines:
   - libfuzzer
   - honggfuzz
diff --git a/projects/binutils/project.yaml b/projects/binutils/project.yaml
index 9e802555a048..fbb1becb5559 100644
--- a/projects/binutils/project.yaml
+++ b/projects/binutils/project.yaml
@@ -1,5 +1,5 @@
 homepage: "https://www.gnu.org/software/binutils/"
-main_repo: "https://github.com/bminor/binutils-gdb"
+main_repo: "https://sourceware.org/git/binutils-gdb"
 language: c++
 primary_contact: "bug-binutils@gnu.org"
 auto_ccs :
diff --git a/projects/bs4/project.yaml b/projects/bs4/project.yaml
index 5f023556efd7..83a28ef97f47 100644
--- a/projects/bs4/project.yaml
+++ b/projects/bs4/project.yaml
@@ -1,5 +1,5 @@
 homepage: "https://www.crummy.com/software/BeautifulSoup/"
-main_repo: "https://code.launchpad.net/~leonardr/beautifulsoup/bs4"
+main_repo: "https://git.launchpad.net/beautifulsoup"
 language: python
 primary_contact: "leonard.richardson@gmail.com"
 auto_ccs:
diff --git a/projects/cbor-java/project.yaml b/projects/cbor-java/project.yaml
index 4ed6e445c149..b3d104b02fc3 100644
--- a/projects/cbor-java/project.yaml
+++ b/projects/cbor-java/project.yaml
@@ -1,7 +1,7 @@
 homepage: "https://android.googlesource.com/platform/external/cbor-java/+/refs/heads/master"
 language: jvm
 primary_contact: "constantin.rack@gmail.com"
-main_repo: "https://android.googlesource.com/platform/external/cbor-java/+/refs/heads/master"
+main_repo: "https://android.googlesource.com/platform/external/cbor-java"
 auto_ccs:
   - "david@adalogics.com"
 fuzzing_engines:
diff --git a/projects/cryptofuzz/project.yaml b/projects/cryptofuzz/project.yaml
index 77668acbbd30..3052b578857e 100644
--- a/projects/cryptofuzz/project.yaml
+++ b/projects/cryptofuzz/project.yaml
@@ -44,7 +44,7 @@ sanitizers:
   - memory
 architectures:
   - x86_64
-main_repo: 'https://github.com/guidovranken/cryptofuzz'
+main_repo: "https://github.com/MozillaSecurity/cryptofuzz"
 
 fuzzing_engines:
   - afl
diff --git a/projects/dapr/project.yaml b/projects/dapr/project.yaml
index a23aa507f5c9..1ef080fecda2 100644
--- a/projects/dapr/project.yaml
+++ b/projects/dapr/project.yaml
@@ -2,7 +2,7 @@ base_os_version: ubuntu-24-04
 homepage: "https://dapr.io/"
 language: go
 primary_contact: "schneideryaron@gmail.com"
-main_repo: "https://github.com/dapr"
+main_repo: "https://github.com/dapr/dapr"
 auto_ccs:
   - "artur04@gmail.com"
 vendor_ccs:
diff --git a/projects/example/project.yaml b/projects/example/project.yaml
index 5bc33721c6e5..9edf5b6367db 100644
--- a/projects/example/project.yaml
+++ b/projects/example/project.yaml
@@ -1,6 +1,6 @@
 disabled: true
 homepage: https://my-api.example.com
-main_repo: https://github.com/example/my-api
+main_repo: "https://github.com/google/oss-fuzz"
 language: c++
 vendor_ccs: []
 
diff --git a/projects/go-cmp/project.yaml b/projects/go-cmp/project.yaml
index f29b4ceb8008..3ac7dbc314a3 100644
--- a/projects/go-cmp/project.yaml
+++ b/projects/go-cmp/project.yaml
@@ -1,6 +1,6 @@
 homepage: "https://github.com/google/go-cmp/cmp"
 language: go
-main_repo: "https://github.com/google/go-cmp/cmp"
+main_repo: "https://github.com/google/go-cmp"
 auto_ccs:
   - "adam@adalogics.com"
 fuzzing_engines:
diff --git a/projects/hive/project.yaml b/projects/hive/project.yaml
index 9f5dc7aaef63..7834020dec91 100644
--- a/projects/hive/project.yaml
+++ b/projects/hive/project.yaml
@@ -3,7 +3,7 @@ homepage: "https://hive.apache.org/"
 language: jvm
 fuzzing_engines:
   - libfuzzer
-main_repo: "https://github.com/apache/hive/tree/master/"
+main_repo: "https://github.com/apache/hive"
 sanitizers:
   - address
 vendor_ccs:
diff --git a/projects/hostap/project.yaml b/projects/hostap/project.yaml
index c5e0854d3b7b..500bd568415b 100644
--- a/projects/hostap/project.yaml
+++ b/projects/hostap/project.yaml
@@ -15,4 +15,4 @@ sanitizers:
 architectures:
   - x86_64
   - i386
-main_repo: 'git://w1.fi/srv/git/hostap.git'
+main_repo: "https://w1.fi/hostap.git"
diff --git a/projects/hyperium/project.yaml b/projects/hyperium/project.yaml
index c3d3d9fc2443..38edfa3822ca 100644
--- a/projects/hyperium/project.yaml
+++ b/projects/hyperium/project.yaml
@@ -1,5 +1,5 @@
 homepage: "https://github.com/hyperium/"
-main_repo: "https://github.com/hyperium/"
+main_repo: "https://github.com/hyperium/http"
 primary_contact: "sean.monstar@gmail.com"
 sanitizers:
   - address
diff --git a/projects/knative/project.yaml b/projects/knative/project.yaml
index 3671d8e79c11..d28e046a4640 100644
--- a/projects/knative/project.yaml
+++ b/projects/knative/project.yaml
@@ -1,7 +1,7 @@
 homepage: "https://knative.dev/"
 language: go
 primary_contact: "security@knative.team"
-main_repo: "https://github.com/knative"
+main_repo: "https://github.com/knative/serving"
 vendor_ccs:
   - "adam@adalogics.com"
   - "david@adalogics.com"
diff --git a/projects/libpng-proto/project.yaml b/projects/libpng-proto/project.yaml
index 5c34acfa0820..8003a30feeea 100644
--- a/projects/libpng-proto/project.yaml
+++ b/projects/libpng-proto/project.yaml
@@ -1,5 +1,5 @@
 homepage: "http://www.libpng.org/pub/png/libpng.html"
-main_repo: "https://git.code.sf.net/p/libpng/code libpng-code"
+main_repo: "https://github.com/pnggroup/libpng.git"
 language: c++
 primary_contact: "kcc@google.com"
 sanitizers:
diff --git a/projects/libtheora/project.yaml b/projects/libtheora/project.yaml
index 330ed43d0f05..46e36ddaee7e 100644
--- a/projects/libtheora/project.yaml
+++ b/projects/libtheora/project.yaml
@@ -1,7 +1,7 @@
 homepage: "https://www.theora.org/"
 language: c++
 primary_contact: "guidovranken@gmail.com"
-main_repo: "https://git.xiph.org/theora.git"
+main_repo: "https://gitlab.xiph.org/xiph/theora"
 auto_ccs:
   - "le.businessman@gmail.com"
 vendor_ccs:
diff --git a/projects/mupdf/project.yaml b/projects/mupdf/project.yaml
index 70bb83258615..2e3a70daaf10 100644
--- a/projects/mupdf/project.yaml
+++ b/projects/mupdf/project.yaml
@@ -1,4 +1,4 @@
-main_repo: git://git.ghostscript.com/mupdf.git
+main_repo: "https://github.com/ArtifexSoftware/mupdf.git"
 homepage: "https://www.mupdf.com"
 language: c++
 primary_contact: tor.andersson@artifex.com
diff --git a/projects/net-snmp/project.yaml b/projects/net-snmp/project.yaml
index 7921811e620e..b847f7bcb404 100644
--- a/projects/net-snmp/project.yaml
+++ b/projects/net-snmp/project.yaml
@@ -7,7 +7,7 @@ auto_ccs:
    - "bvanassche@acm.org"
    - "magfr@lysator.liu.se"
    - "david@adalogics.com"
-main_repo: 'git://git.code.sf.net/p/net-snmp/code'
+main_repo: "https://github.com/net-snmp/net-snmp"
 fuzzing_engines:
   - afl
   - honggfuzz
diff --git a/projects/notary/project.yaml b/projects/notary/project.yaml
index 041a57a3c1ae..71a00c7269ed 100644
--- a/projects/notary/project.yaml
+++ b/projects/notary/project.yaml
@@ -1,5 +1,5 @@
 homepage: "https://github.com/notaryproject/notary"
-main_repo: "https://github.com/notaryproject"
+main_repo: "https://github.com/notaryproject/notary"
 primary_contact: "yizha1@microsoft.com"
 auto_ccs :
   - "vaninrao@amazon.com"
diff --git a/projects/ntp/project.yaml b/projects/ntp/project.yaml
index 85dba5e72270..5fc0a1fb698c 100644
--- a/projects/ntp/project.yaml
+++ b/projects/ntp/project.yaml
@@ -1,7 +1,7 @@
 homepage: "http://www.ntp.org"
 language: c++
 primary_contact: "security@ntp.org"
-main_repo: "https://bitbucket.nwtime.org/pc/ntp.git"
+main_repo: "https://github.com/ntp-project/ntp"
 auto_ccs:
   - "p.antoine@catenacyber.fr"
 fuzzing_engines:
diff --git a/projects/pidgin/project.yaml b/projects/pidgin/project.yaml
index 9b277e55fe16..7a20ad6b69fe 100644
--- a/projects/pidgin/project.yaml
+++ b/projects/pidgin/project.yaml
@@ -4,7 +4,7 @@ language: c
 auto_ccs:
   - "quantum.analyst@gmail.com"
   - "rekkanoryo.guifications@gmail.com"
-main_repo: 'https://sourceforge.net/projects/pidgin/files/Pidgin/2.14.4/pidgin-2.14.4.tar.bz2'
+main_repo: "https://github.com/pidgin/pidgin"
 
 fuzzing_engines:
   - afl
diff --git a/projects/piex/project.yaml b/projects/piex/project.yaml
index 6c853bcafe5f..478b16025772 100644
--- a/projects/piex/project.yaml
+++ b/projects/piex/project.yaml
@@ -5,4 +5,4 @@ sanitizers:
  - address
  - undefined
  - memory
-main_repo: 'https://github.com/guidovranken/piex.git'
+main_repo: "https://android.googlesource.com/platform/external/piex"
diff --git a/projects/postgresql/project.yaml b/projects/postgresql/project.yaml
index 975e8e500661..9fb986213a03 100644
--- a/projects/postgresql/project.yaml
+++ b/projects/postgresql/project.yaml
@@ -1,6 +1,6 @@
 base_os_version: ubuntu-24-04
 homepage: "https://postgresql.org"
-main_repo: "https://git.postgresql.org/git/postgresql"
+main_repo: "https://github.com/postgres/postgres"
 primary_contact: "sfrost@snowman.net"
 language: c
 auto_ccs:
diff --git a/projects/qubes-os/project.yaml b/projects/qubes-os/project.yaml
index 073b4cde0fcb..88161a8fb5f9 100644
--- a/projects/qubes-os/project.yaml
+++ b/projects/qubes-os/project.yaml
@@ -1,5 +1,5 @@
 homepage: "https://www.qubes-os.org/"
-main_repo: "https://github.com/QubesOS"
+main_repo: "https://github.com/QubesOS/qubes-app-linux-input-proxy"
 language: c++
 primary_contact: "jpo@vt.edu"
 auto_ccs:
diff --git a/projects/radvd/project.yaml b/projects/radvd/project.yaml
index 986f4b76aaf2..cfcdb95b3e91 100644
--- a/projects/radvd/project.yaml
+++ b/projects/radvd/project.yaml
@@ -10,5 +10,5 @@ auto_ccs:
 - "david@adalogics.com"
 - "cloud-ti-fuzzing+bugs@google.com"
 
-main_repo: "http://www.litech.org/radvd"
+main_repo: "https://github.com/radvd-project/radvd"
 base_os_version: ubuntu-24-04
diff --git a/projects/sqlite3/project.yaml b/projects/sqlite3/project.yaml
index b16a07101974..ca12f004c453 100644
--- a/projects/sqlite3/project.yaml
+++ b/projects/sqlite3/project.yaml
@@ -1,5 +1,5 @@
 homepage: "https://sqlite.org/"
-main_repo: "https://sqlite.org/src/dir"
+main_repo: "https://github.com/sqlite/sqlite"
 language: c++
 primary_contact: "drhsqlite@gmail.com"
 auto_ccs:
diff --git a/projects/stax/project.yaml b/projects/stax/project.yaml
index 4701c7d32a7b..6cef1ccb6e94 100644
--- a/projects/stax/project.yaml
+++ b/projects/stax/project.yaml
@@ -1,6 +1,6 @@
 homepage: "https://docs.oracle.com/javase/8/docs/api/index.html?javax/xml/stream/package-summary.html"
 language: jvm
-main_repo: "https://github.com/openjdk/jdk/tree/master/src/java.xml/share/classes"
+main_repo: "https://github.com/openjdk/jdk"
 fuzzing_engines:
   - libfuzzer
 sanitizers:
diff --git a/projects/unicode-rs/project.yaml b/projects/unicode-rs/project.yaml
index 914c14551297..bf67129676a1 100644
--- a/projects/unicode-rs/project.yaml
+++ b/projects/unicode-rs/project.yaml
@@ -1,5 +1,5 @@
 homepage: "http://unicode-rs.github.io/"
-main_repo: "https://github.com/unicode-rs"
+main_repo: "https://github.com/unicode-rs/unicode-normalization"
 primary_contact: "manishsmail@gmail.com"
 sanitizers:
   - address