diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
index cbf56a2..8fa3240 100644
--- a/.github/workflows/pypi-publish.yml
+++ b/.github/workflows/pypi-publish.yml
@@ -1,7 +1,7 @@
 # This workflows will upload a Python Package using poetry when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
-name: Publish RSMetaCheck package to PyPI
+name: Publish rsmetacheck package to PyPI
 
 on:
   workflow_dispatch: 
diff --git a/README.md b/README.md
index 108e4f8..4c856e0 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ MetaCheck identifies **29 different types of metadata quality issues** across mu
 (Python, Java, C++, C, R, Rust). These pitfalls range from version mismatches and
 license template placeholders to broken URLs and improperly formatted metadata fields.
 
-You can visit our [catalog](https://softwareunderstanding.github.io/RsMetaCheck/) to see in details what these pitfalls are, where are they usually detected and how to fix them.
+You can visit our [catalog](https://softwareunderstanding.github.io/rsmetacheck/) to see in details what these pitfalls are, where are they usually detected and how to fix them.
 
 ### Supported Pitfall Types
 
@@ -45,8 +45,8 @@ The tool detects the following categories of issues:
 1. **Clone the repository**:
 
    ```bash
-   git clone https://github.com/SoftwareUnderstanding/RsMetaCheck.git
-   cd RsMetaCheck
+   git clone https://github.com/SoftwareUnderstanding/rsmetacheck.git
+   cd rsmetacheck
    ```
 
 2. **Install with Poetry**:
@@ -67,7 +67,7 @@ The tool detects the following categories of issues:
 Alternatively, you can install directly from GitHub:
 
 ```bash
-pip install git+https://github.com/SoftwareUnderstanding/RsMetaCheck.git
+pip install git+https://github.com/SoftwareUnderstanding/rsmetacheck.git
 ```
 
 ## Usage
diff --git a/codemeta.json b/codemeta.json
index 369abb0..8aacbce 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -14,16 +14,16 @@
       "givenName": "Anas"
     }
   ],
-  "codeRepository": "git+https://github.com/SoftwareUnderstanding/RsMetaCheck.git",
+  "codeRepository": "git+https://github.com/SoftwareUnderstanding/rsmetacheck.git",
   "dateModified": "2026-07-22",
   "description": "Automated tool to detect metadata quality pitfalls in software repositories (Python, Java, C++, etc.). Analyzes SoMEF output files for version mismatches, license issues, broken URLs, and more. ",
-  "downloadUrl": "https://github.com/SoftwareUnderstanding/RsMetaCheck/archive/refs/heads/main.tar.gz",
+  "downloadUrl": "https://github.com/SoftwareUnderstanding/rsmetacheck/archive/refs/heads/main.tar.gz",
   "keywords": ["codemeta", "pitfalls", "metadata", "analysis"],
   "license": "https://spdx.org/licenses/MIT",
-  "name": "RsMetaCheck",
+  "name": "rsmetacheck",
   "operatingSystem": "Linux",
   "programmingLanguage": "Python",
   "version": "0.3.5",
   "developmentStatus": "active",
-  "issueTracker": "https://github.com/SoftwareUnderstanding/RsMetaCheck/issues"
+  "issueTracker": "https://github.com/SoftwareUnderstanding/rsmetacheck/issues"
 }
diff --git a/data/examples/notes_example.json b/data/examples/notes_example.json
index 40adeec..d437dce 100644
--- a/data/examples/notes_example.json
+++ b/data/examples/notes_example.json
@@ -2,7 +2,7 @@
   "total_notes": 1,
   "notes": [
     {
-      "repository": "SoftwareUnderstanding/RsMetaCheck",
+      "repository": "SoftwareUnderstanding/rsmetacheck",
       "file_name": "output_1.json",
       "code": "P001",
       "note": "Version discrepancy: codemeta.json '0.3.2dev' vs release '0.3.1'"
diff --git a/docs/catalog.html b/docs/catalog.html
index db07821..284f532 100644
--- a/docs/catalog.html
+++ b/docs/catalog.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="UTF-8">
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  <title>RsMetaCheck Catalog</title>
+  <title>rsmetacheck Catalog</title>
 
   <!-- DataTables CSS -->
   <link rel="stylesheet" href="https://cdn.datatables.net/1.13.6/css/jquery.dataTables.min.css">
@@ -179,7 +179,7 @@ <h1>Metadata Pitfalls &amp; Warnings Catalog</h1>
     <p>
       This is a catalog of the pitfalls and warnings we have come across during our research on software metadata quality.
       Based on these findings, we at <a href="https://oeg.fi.upm.es/" target="_blank">Ontology Engineering Group (OEG)</a>
-      have developed our tool <strong><a href="https://github.com/SoftwareUnderstanding/RsMetaCheck" target="_blank">RSMetaCheck</a></strong> to automatically diagnose and identify these common issues in software metadata files.
+      have developed our tool <strong><a href="https://github.com/SoftwareUnderstanding/rsmetacheck" target="_blank">rsmetacheck</a></strong> to automatically diagnose and identify these common issues in software metadata files.
       Warnings do not have a severity level because originally they were opted due to their low severity and classified as "Warnings" instead of "Pitfalls"
     </p>
   </div>
diff --git a/docs/ground_truth/charts.html b/docs/ground_truth/charts.html
index da08918..cedd89a 100644
--- a/docs/ground_truth/charts.html
+++ b/docs/ground_truth/charts.html
@@ -3,7 +3,7 @@
 <head>
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>RsMetaCheck &mdash; 0.3.0 vs 0.3.5 Charts</title>
+    <title>rsmetacheck &mdash; 0.3.0 vs 0.3.5 Charts</title>
     <style>
         body {
             font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
@@ -80,7 +80,7 @@ <h1>0.3.0 vs 0.3.5 &mdash; Charts</h1>
 
     <p style="text-align: center; color: #555; font-size: 0.95em; line-height: 1.5; max-width: 800px; margin: 0 auto 20px auto;">
         Pitfall and warning detection distributions across 150 repositories evaluated by
-        RsMetaCheck versions 0.3.0 and 0.3.5.
+        rsmetacheck versions 0.3.0 and 0.3.5.
     </p>
 
     <hr class="section-divider">
diff --git a/docs/ground_truth/comparison.html b/docs/ground_truth/comparison.html
index 31222b2..d1cb056 100644
--- a/docs/ground_truth/comparison.html
+++ b/docs/ground_truth/comparison.html
@@ -3,7 +3,7 @@
 <head>
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>RsMetaCheck &mdash; 0.3.0 vs 0.3.5 Comparison</title>
+    <title>rsmetacheck &mdash; 0.3.0 vs 0.3.5 Comparison</title>
     <style>
         body {
             font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
@@ -125,9 +125,9 @@
     <h1>0.3.0 vs 0.3.5 &mdash; Comparison</h1>
 
     <p style="text-align: center; color: #555; font-size: 0.95em; line-height: 1.5; max-width: 800px; margin: 0 auto 20px auto;">
-        This page compares the detection results of RsMetaCheck version 0.3.0 and
+        This page compares the detection results of rsmetacheck version 0.3.0 and
         version 0.3.5 across 150 repositories. What is highlighed in red is what was previously falsly flagged and fixed in the latest
-        release, and what is highlighted in green is what was not being detected in the ealier version of RSMetaCheck and fixed in the latest
+        release, and what is highlighted in green is what was not being detected in the ealier version of rsmetacheck and fixed in the latest
         release.
     </p>
 
diff --git a/docs/ground_truth/index.html b/docs/ground_truth/index.html
index 777bfdc..53ebf30 100644
--- a/docs/ground_truth/index.html
+++ b/docs/ground_truth/index.html
@@ -3,7 +3,7 @@
 <head>
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>RsMetaCheck Pitfalls Report</title>
+    <title>rsmetacheck Pitfalls Report</title>
     <style>
         body {
             font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
diff --git a/docs/index.html b/docs/index.html
index 3709536..9ec40ab 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -3,7 +3,7 @@
 <head>
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>RsMetaCheck</title>
+    <title>rsmetacheck</title>
     <style>
         body {
             font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
@@ -96,14 +96,14 @@
         })();
     </script>
     <div class="container">
-        <h1>RsMetaCheck Study</h1>
+        <h1>rsmetacheck Study</h1>
         <p class="subtitle">
-            <a href="https://github.com/SoftwareUnderstanding/RsMetaCheck">RsMetaCheck</a> is an automated tool built to detect metadata quality pitfalls in software repositories, from version mismatches, license issues, 
+            <a href="https://github.com/SoftwareUnderstanding/rsmetacheck">rsmetacheck</a> is an automated tool built to detect metadata quality pitfalls in software repositories, from version mismatches, license issues, 
             broken URLs using <a href="https://github.com/KnowledgeCaptureAndDiscovery/somef">SoMEF</a> extraction  capabilities. We built a catalog of the issues we documented 
             throughout our study, classsifed in two categories: <b>Pitfalls</b> and <b>Warnings</b> based on the severity of the issue and the consensus reached between domain experts. To verify 
             the performance of our tool we made for this study, we built a ground truth dataset based on a sample of 150 repositories sampled from a dataset of repositories that consists of  
             <a href="https://github.com/TheOSSci/InnovationSprint2025_Extending_Software_Metadata">InnovationSprint2025</a> and a small sample of openAIRE, amounting to a total of 1500 repositories, then had 
-            RSMetaCheck tested using version 0.3.0 and 0.3.5 (To evaluate the progress of our perfromance) with comparison to the ground truth that we have established.
+            rsmetacheck tested using version 0.3.0 and 0.3.5 (To evaluate the progress of our perfromance) with comparison to the ground truth that we have established.
         </p>
         <div class="cards">
             <a href="catalog.html" class="card">
diff --git a/docs/index.md b/docs/index.md
index 92a54a9..69c63b9 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,12 +1,12 @@
-# Research Metadata Check (RSMetaCheck) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18956787.svg)](https://doi.org/10.5281/zenodo.18956787) [![PyPI - Version](https://img.shields.io/pypi/v/rsmetacheck)](https://pypi.org/project/rsmetacheck/)
+# Research Metadata Check (rsmetacheck) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18956787.svg)](https://doi.org/10.5281/zenodo.18956787) [![PyPI - Version](https://img.shields.io/pypi/v/rsmetacheck)](https://pypi.org/project/rsmetacheck/)
 
-**RSMetaCheck** is an automated tool for detecting common metadata quality issues (pitfalls & warnings) in software repositories.
+**rsmetacheck** is an automated tool for detecting common metadata quality issues (pitfalls & warnings) in software repositories.
 The tool analyzes SoMEF (Software Metadata Extraction Framework) output files to identify various problems in repository metadata
 files such as `codemeta.json`, `package.json`, `setup.py`, `DESCRIPTION`, and others.
 
 ## Features
 
-RSMetaCheck identifies **29 different types of metadata quality issues** across multiple programming languages (Python, Java, C++, C, R, Rust).
+rsmetacheck identifies **29 different types of metadata quality issues** across multiple programming languages (Python, Java, C++, C, R, Rust).
 
 - **Version Consistency**: Detects mismatches between metadata files and actual software releases.
 - **License Validation**: Identifies template placeholders, missing versions, and legal ambiguities in licenses.
diff --git a/docs/installation.md b/docs/installation.md
index 1af4a1d..f44f43e 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -1,14 +1,14 @@
 # Installation
 
-RSMetaCheck requires **Python 3.11**.
+rsmetacheck requires **Python 3.11**.
 
 ## Using Poetry (Recommended)
 
 1. **Clone the repository**:
 
    ```bash
-   git clone https://github.com/SoftwareUnderstanding/RsMetaCheck.git
-   cd RsMetaCheck
+   git clone https://github.com/SoftwareUnderstanding/rsmetacheck.git
+   cd rsmetacheck
    ```
 
 2. **Install with Poetry**:
@@ -30,5 +30,5 @@ RSMetaCheck requires **Python 3.11**.
 Alternatively, you can install directly from GitHub:
 
 ```bash
-pip install git+https://github.com/SoftwareUnderstanding/RsMetaCheck.git
+pip install git+https://github.com/SoftwareUnderstanding/rsmetacheck.git
 ```
diff --git a/docs/output.md b/docs/output.md
index f6f9aa4..4a51baf 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,6 +1,6 @@
 # Output
 
-When you run RSMetaCheck, it generates several files containing the results of the analysis.
+When you run rsmetacheck, it generates several files containing the results of the analysis.
 
 ## Generated Files
 
diff --git a/docs/usage.md b/docs/usage.md
index 16a7aa4..5a384d0 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,6 +1,6 @@
 # Usage
 
-RSMetaCheck can be used as a local command-line tool or integrated into your CI/CD pipeline as a GitHub Action or a GitLab CI/CD job.
+rsmetacheck can be used as a local command-line tool or integrated into your CI/CD pipeline as a GitHub Action or a GitLab CI/CD job.
 
 ## Command Line Interface
 
@@ -43,7 +43,7 @@ poetry run rsmetacheck --input repositories.json
 
 ### Customize Output Paths
 
-By default RSMetaCheck writes its output to the current working directory. Use the flags below to redirect any of the outputs:
+By default rsmetacheck writes its output to the current working directory. Use the flags below to redirect any of the outputs:
 
 | Flag | Default | Description |
 |------|---------|-------------|
@@ -62,7 +62,7 @@ poetry run rsmetacheck --input repositories.json \
 
 ### Version Discrepancy Notes
 
-When a metadata version differs from the release version only slightly (every component differs by less than 2, e.g. `0.4.3.dev1` vs `0.4.2` — the pre-release suffix means it is numerically close), RSMetaCheck records a **note** instead of a full pitfall. Notes are only written when `--notes-output` is provided:
+When a metadata version differs from the release version only slightly (every component differs by less than 2, e.g. `0.4.3.dev1` vs `0.4.2` — the pre-release suffix means it is numerically close), rsmetacheck records a **note** instead of a full pitfall. Notes are only written when `--notes-output` is provided:
 
 ```bash
 poetry run rsmetacheck --input https://github.com/example/repo --notes-output ./notes.json
@@ -126,7 +126,7 @@ poetry run rsmetacheck --input https://github.com/example/repo --generate-codeme
 
 ### Configure Analysis Rules
 
-RSMetaCheck automatically detects a `.rsmetacheck.toml` (or `rsmetacheck.toml`) file at the working directory. Alternatively, supply a custom path with `--config`:
+rsmetacheck automatically detects a `.rsmetacheck.toml` (or `rsmetacheck.toml`) file at the working directory. Alternatively, supply a custom path with `--config`:
 
 ```bash
 poetry run rsmetacheck --input https://github.com/example/repo --config ./ci/rsmetacheck.toml
@@ -174,12 +174,12 @@ poetry run rsmetacheck --input https://github.com/example/repo --config-profile
 
 ## GitHub Action
 
-You can integrate RSMetaCheck into your GitHub workflow to test your own repository and detect issues automatically.
+You can integrate rsmetacheck into your GitHub workflow to test your own repository and detect issues automatically.
 Please refer to our action in the GitHub MarketPlace at [rsmetacheck actions](https://github.com/marketplace/actions/rsmetacheck) for more information.
 
 ## GitLab CI/CD
 
-You can integrate RSMetaCheck into your GitLab pipelines by adding the following snippet to your `.gitlab-ci.yml` file:
+You can integrate rsmetacheck into your GitLab pipelines by adding the following snippet to your `.gitlab-ci.yml` file:
 
 ```yaml
 rsmetacheck:
@@ -220,4 +220,3 @@ rsmetacheck:
     when: always
     expire_in: 1 week
 ```
-
diff --git a/mkdocs.yml b/mkdocs.yml
index 8e949d3..6e2ce40 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: RSMetaCheck
+site_name: rsmetacheck
 theme:
   name: material
 extra_css:
diff --git a/src/rsmetacheck/cli.py b/src/rsmetacheck/cli.py
index dcc9e10..ea1f4c8 100644
--- a/src/rsmetacheck/cli.py
+++ b/src/rsmetacheck/cli.py
@@ -105,7 +105,7 @@ def cli():
     parser.add_argument(
         "--config",
         default=None,
-        help="Path to RsMetaCheck TOML config file (default: auto-detect .rsmetacheck.toml at repository root).",
+        help="Path to rsmetacheck TOML config file (default: auto-detect .rsmetacheck.toml at repository root).",
     )
     parser.add_argument(
         "--config-profile",
diff --git a/src/rsmetacheck/detect_pitfalls_main.py b/src/rsmetacheck/detect_pitfalls_main.py
index 9b86c35..2a032be 100644
--- a/src/rsmetacheck/detect_pitfalls_main.py
+++ b/src/rsmetacheck/detect_pitfalls_main.py
@@ -473,7 +473,7 @@ def detect_all_pitfalls(
                                     if "result" in item and "value" in item["result"]:
                                         repo_name = item["result"]["value"]
                                         break
-                            w3id_code = f"https://softwareunderstanding.github.io/RsMetaCheck/#{pitfall_code}"
+                            w3id_code = f"https://softwareunderstanding.github.io/rsmetacheck/#{pitfall_code}"
                             notes = pitfall_result.get("notes", [])
                             if notes:
                                 for note_entry in notes:
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 134db51..230dbab 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -552,6 +552,17 @@ def test_cli_input_required(monkeypatch):
         pass
 
 
+def test_cli_help_mentions_rsmetacheck_config(monkeypatch, capsys):
+    """Help text should reference the lowercase rsmetacheck config name."""
+    monkeypatch.setattr("sys.argv", ["rsmetacheck", "--help"])
+
+    with pytest.raises(SystemExit):
+        cli_module.cli()
+
+    captured = capsys.readouterr()
+    assert "Path to rsmetacheck TOML config file" in captured.out
+
+
 def test_cli_config_profile_forwarded_to_run_analysis(monkeypatch, tmp_path):
     """--config and --config-profile should load and forward analysis config."""
     somef_file = tmp_path / "somef_output.json"
diff --git a/tests/test_e2e.py b/tests/test_e2e.py
index 3fe1460..d4db6b8 100644
--- a/tests/test_e2e.py
+++ b/tests/test_e2e.py
@@ -158,7 +158,8 @@ def test_notes_output_created_when_specified(self, tmp_path):
         assert notes_file.exists()
         notes_data = json.loads(notes_file.read_text())
         assert "notes" in notes_data
-        assert notes_data["total_notes"] >= 0
+        assert notes_data["total_notes"] == 1
+        assert notes_data["notes"][0]["code"] == "https://softwareunderstanding.github.io/rsmetacheck/#P001"
 
 
 class TestMultipleRepoPipeline:
