From ea3f5574889a0190d86fb05e52de979d477a5bc0 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Wed, 28 Jan 2026 16:00:45 +0000
Subject: [PATCH 1/4] change method of ignoring files

---
 github_scripts/get_git_sources.py | 29 +++++++++--------------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/github_scripts/get_git_sources.py b/github_scripts/get_git_sources.py
index 323afbed..66a64aad 100644
--- a/github_scripts/get_git_sources.py
+++ b/github_scripts/get_git_sources.py
@@ -134,26 +134,15 @@ def sync_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
     # Create a clean clone location
     loc.mkdir(parents=True)
 
-    exclude_dirs = (
-        "applications/*/working",
-        "applications/*/test",
-        "applications/*/bin",
-        "science/*/working",
-        "science/*/test",
-        "science/*/bin",
-        "interfaces/*/working",
-        "interfaces/*/test",
-        "interfaces/*/bin",
-        "components/*/working",
-        "components/*/test",
-        "components/*/bin",
-        "infrastructure/*/working",
-        "infrastructure/*/test",
-        "infrastructure/*/bin",
-        "mesh_tools/*/working",
-        "mesh_tools/*/test",
-        "mesh_tools/*/bin",
-    )
+    exclude_dirs = []
+    result = run_command(f"git -C {repo_source} --ignored -s")
+    for ignore_file in result.stdout.split():
+        ignore_file = ignore_file.strip()
+        if not ignore_file.startswith("!!"):
+            continue
+        ignore_file = ignore_file.removeprefix("!!")
+        ignore_file = ignore_file.strip()
+        exclude_dirs.append(ignore_file)
 
     # Trailing slash required for rsync
     command = f"rsync -av {repo_source}/ {loc}"

From a68191c92d46bfebe43c3b5ce8d0eab8d31a13c9 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Thu, 29 Jan 2026 08:42:18 +0000
Subject: [PATCH 2/4] update to use ssh

---
 github_scripts/get_git_sources.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/github_scripts/get_git_sources.py b/github_scripts/get_git_sources.py
index 66a64aad..87e76414 100644
--- a/github_scripts/get_git_sources.py
+++ b/github_scripts/get_git_sources.py
@@ -135,7 +135,8 @@ def sync_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
     loc.mkdir(parents=True)
 
     exclude_dirs = []
-    result = run_command(f"git -C {repo_source} --ignored -s")
+    host, path = repo_source.split(":", 1)
+    result = run_command(f"ssh {host} git -C {repo_source} status --ignored -s")
     for ignore_file in result.stdout.split():
         ignore_file = ignore_file.strip()
         if not ignore_file.startswith("!!"):

From e2d3c04d8ac6ba991cb2af36223339c4a2a61dd3 Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Thu, 29 Jan 2026 08:43:42 +0000
Subject: [PATCH 3/4] debug message

---
 github_scripts/get_git_sources.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/github_scripts/get_git_sources.py b/github_scripts/get_git_sources.py
index 87e76414..c1c41a1c 100644
--- a/github_scripts/get_git_sources.py
+++ b/github_scripts/get_git_sources.py
@@ -136,7 +136,7 @@ def sync_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
 
     exclude_dirs = []
     host, path = repo_source.split(":", 1)
-    result = run_command(f"ssh {host} git -C {repo_source} status --ignored -s")
+    result = run_command(f"ssh {host} git -C {path} status --ignored -s")
     for ignore_file in result.stdout.split():
         ignore_file = ignore_file.strip()
         if not ignore_file.startswith("!!"):
@@ -144,6 +144,7 @@ def sync_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
         ignore_file = ignore_file.removeprefix("!!")
         ignore_file = ignore_file.strip()
         exclude_dirs.append(ignore_file)
+    print(exclude_dirs)
 
     # Trailing slash required for rsync
     command = f"rsync -av {repo_source}/ {loc}"

From 577e54c9b1468321a862618d009290f264028c3b Mon Sep 17 00:00:00 2001
From: James Bruten <109733895+james-bruten-mo@users.noreply.github.com>
Date: Thu, 29 Jan 2026 09:16:53 +0000
Subject: [PATCH 4/4] fix split

---
 github_scripts/get_git_sources.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/github_scripts/get_git_sources.py b/github_scripts/get_git_sources.py
index c1c41a1c..ca233975 100644
--- a/github_scripts/get_git_sources.py
+++ b/github_scripts/get_git_sources.py
@@ -137,14 +137,12 @@ def sync_repo(repo_source: str, repo_ref: str, loc: Path) -> None:
     exclude_dirs = []
     host, path = repo_source.split(":", 1)
     result = run_command(f"ssh {host} git -C {path} status --ignored -s")
-    for ignore_file in result.stdout.split():
+    for ignore_file in result.stdout.split("\n"):
         ignore_file = ignore_file.strip()
         if not ignore_file.startswith("!!"):
             continue
-        ignore_file = ignore_file.removeprefix("!!")
-        ignore_file = ignore_file.strip()
+        ignore_file = ignore_file.removeprefix("!!").strip()
         exclude_dirs.append(ignore_file)
-    print(exclude_dirs)
 
     # Trailing slash required for rsync
     command = f"rsync -av {repo_source}/ {loc}"