diff --git a/.markdown-link-check.json b/.github/.markdown-link-check.json
similarity index 100%
rename from .markdown-link-check.json
rename to .github/.markdown-link-check.json
diff --git a/.markdownlint.yaml b/.github/.markdownlint.yaml
similarity index 81%
rename from .markdownlint.yaml
rename to .github/.markdownlint.yaml
index fcf3de2f04..1ceecef4ef 100644
--- a/.markdownlint.yaml
+++ b/.github/.markdownlint.yaml
@@ -12,7 +12,3 @@ MD013:
 MD024:
   # Allow heading duplication if under different parent headings
   siblings_only: true
-
-# MD030:
-#     ul_single: 3
-#     ul_multi: 3
diff --git a/.gitignore b/.gitignore
index 50fade5a57..06f49c7f26 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,37 +1,45 @@
+# Rust / Cargo
 target/
 .cargo_check/
-.history/
-*.swp
-TODO.md
-data/html
+rustc-ice*.txt
+crate/server/Cargo.toml.bak
+vendor/
+# Security / Secrets
 data/keys
 .env
-.venv/
+# Runtime artifacts / Local Data
+data/html
+crate/cli/*.sqlite
+**/*cosmian-kms/sqlite-data*
+http_cache.sqlite
+result*
+sbom.*
+resources/cli.zip
 **/data/private
 **/data/public
 **/data/shared
-crate/cli/*.sqlite
-.DS_Store
-.idea/
-rustc-ice*.txt
-node_modules/
-# this directory may contain sqlite data when the KMS is launched locally
-**/*cosmian-kms/sqlite-data*
-run.sh
-.aider/
 .cache
-.local
+# HSM / Crypto Libraries
 .openssl
 resources/tarballs/openssl-3.1.2.tar.gz
 .utimaco
 .softhsm2
 *.xz*
-result*
-crate/server/Cargo.toml.bak
+# UI / Node
+node_modules/
 crate/server/ui*
 ui_non_fips/
-vendor/
-http_cache.sqlite
-sbom.*
-resources/cli.zip
+# OS / IDE / AI
+.DS_Store
+.idea/
+*.swp
+.history/
+.aider/
 .claude
+.vscode/
+.agent/
+.agents/
+# Other
+TODO.md
+.venv/
+.local
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4cc00caf18..a4bdd10eb7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -23,6 +23,7 @@ repos:
       - id: markdownlint-fix
         args:
           [
+            --config=.github/.markdownlint.yaml,
             --disable=MD013,
             --disable=MD033,
             --disable=MD041,
@@ -239,12 +240,12 @@ repos:
       - id: nightly-clippy-autofix-all-targets
       - id: clippy-all-targets-all-features
       - id: clippy-all-targets
-      - id: cargo-format # in last du to clippy fixes
+      - id: cargo-format # in last due to clippy fixes
       - id: docker-compose-down
 
   - repo: https://github.com/tcort/markdown-link-check
     rev: v3.13.7
     hooks:
       - id: markdown-link-check
-        args: [-q, --config, .markdown-link-check.json]
+        args: [-q, --config, ./.markdown-link-check.json]
         exclude: .github/copilot-instructions.md
diff --git a/.vale.ini b/.vale.ini
deleted file mode 100644
index 7e20a20473..0000000000
--- a/.vale.ini
+++ /dev/null
@@ -1,7 +0,0 @@
-StylesPath = .vale-styles
-
-MinAlertLevel = suggestion
-
-[*.md]
-BasedOnStyles = Vale
-Vale.Spelling = NO
diff --git a/_typos.toml b/_typos.toml
deleted file mode 100644
index ecc0b008e3..0000000000
--- a/_typos.toml
+++ /dev/null
@@ -1,5 +0,0 @@
-[default.extend-words]
-GOST = "GOST"
-vas = "vas"
-passin = "passin"
-typ = "typ"
diff --git a/dotenv b/dotenv
deleted file mode 100644
index cb0c39ed9e..0000000000
--- a/dotenv
+++ /dev/null
@@ -1 +0,0 @@
-KMS_SQLITE_PATH = "data/shared"