Clean up Git status

BNR info-hub Technical Manual

1 Clean up Git status

1.1 Purpose

Use this guide before committing changes to the BNR info-hub repository.

The goal is to commit only intentional source files, approved public outputs, and documentation updates.

Do not commit private data, local configuration, generated site output, caches, logs, or temporary files.

2 Stage 1: Check Git status

cd C:\yoshimi-hot\output\analyse-bnr\info-hub
git status

For a shorter view:

git status -s

3 Stage 2: Know what should usually be tracked

Expected tracked changes may include:

scripts/stata/
site/
site/downloads/files/
outputs/public/
README.md
DECISIONS.md
CHANGELOG.md

For the case-count pilot, expected tracked changes may include:

scripts/stata/briefings/cvd_cases_2023/cvd_cases_2023.do
scripts/stata/common/bnrcvd_prep_2023_v1.do
scripts/stata/common/bnrcvd_globals.do
outputs/public/briefings/cvd_cases_2023_v1/
site/downloads/files/briefings/cvd_cases_2023_v1/
site/surveillance/cvd/briefings/case-counts.qmd
site/surveillance/cvd/briefings/case-counts-pdf.qmd
site/technical/
site/operations-manual/

4 Stage 3: Know what should not be tracked

These should normally not be committed:

site/_site/
site/.quarto/
site/_freeze/
local-setup-notes.md
scripts/stata/config/bnr_paths_LOCAL.do
info-hub-private/
*.dta
*.log
*.smcl
*.gph

Confidential source data and private working files must stay outside the repo in:

C:\yoshimi-hot\output\analyse-bnr\info-hub-private\

They should never appear in Git status.

5 Stage 4: Check ignored files if needed

To check whether a file is ignored:

git check-ignore -v path\to\file

Example:

git check-ignore -v scripts\stata\config\bnr_paths_LOCAL.do

This should show that the local path file is ignored.

6 Stage 5: Stage only intended files

Stage by folder or file:

git add scripts\stata

git add outputs\public

git add site\surveillance\cvd\briefings

git add site\downloads

git add site\technical

git add site\operations-manual

Then check status again:

git status

Avoid:

git add .

unless you have already checked that no unwanted files appear in Git status.

7 Stage 6: Commit with a clear message

Example:

git commit -m "Add static CVD case-count briefing workflow"

For documentation-only changes:

git commit -m "Add technical manual troubleshooting guides"

8 Stage 7: Final safety check before push

Before pushing, run:

git status

Expected result:

nothing to commit, working tree clean

Then push:

git push
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