Update docs with new/updated commands and usage

Author: dylanhand

README.md

@@ -97,7 +97,7 @@ Then there are some use cases with example commands
 gut clone -o myorg -r "^api-.*"
 
 # Pull all repos across all organizations
-gut pull --all-orgs
+gut pull --all-owners
 
 # Fetch and check status of all repos matching regex
 gut status -r ".*" --fetch
@@ -141,6 +141,9 @@ Commands:
   push      Push the provided branch to remote server for all repositories that match a pattern or a topic
   remove    Remove users (from an organisation or team) or delete repositories
   rename    Rename repositories or teams
+  rename
+    repo          Rename a repository
+    team          Rename a team in an organisation
   set       Set information, secret for repositories or permission for a team
   show      Show config, repositories, members, or user access
   status    Show git status of all repositories that match a pattern
@@ -206,6 +209,7 @@ set
 show
     config        Show current configuration
     repositories  Show all repositories that match a pattern [aliases: repos]
+    repository    Show details for a specific repository (teams, collaborators)
     access        Show repositories accessible by specified user(s) in an organisation
     members       Show all members in an organisation [aliases: users]
     teams         Show all teams in an organisation
@@ -219,7 +223,7 @@ template
 topic
     add           Add topics for all repositories that match a regex
     apply         Apply a script to all repositories that have topics matching a pattern
-    get           Get topics for all repositories that match a regex
+    list          List topics for all repositories that match a regex
     set           Set topics for all repositories that match a regex
 
 workflow

USAGE.md

@@ -260,13 +260,13 @@ FLAGS:
 
 SUBCOMMANDS:
     add
-    get
+    list
     help    Prints this message or the help of the given subcommand(s)
     set     Set topics for all repositories that match a regex
 
 ```
 
-### Topic Get
+### Topic List
 
 ```
 gut-topic-list 0.1.0

docs/docs/get-started.md

@@ -75,18 +75,18 @@ gut init -r ~/gut-repos -t ghp_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
 
 This creates a configuration file in your system's config directory (e.g., `~/.config/gut/` on Linux/macOS).
 
-### 3. Set a Default Organization (Optional)
+### 3. Set a Default Owner (Optional)
 
-To avoid specifying `-o <organization>` with every command, set a default:
+To avoid specifying `-o <owner>` with every command, set a default:
 
 ```bash
-gut set organisation -o <org-name>
+gut set owner <owner-name>
 ```
 
 For example:
 
 ```bash
-gut set organisation -o divvun
+gut set owner divvun
 ```
 
 ## SSH Access (Optional)

docs/docs/usage/common-commands.md

@@ -305,7 +305,7 @@ gut push -o myorg -r ".*"
 Avoid typing `-o <org>` every time:
 
 ```bash
-gut set organisation myorg
+gut set owner myorg
 
 # Now you can omit -o:
 gut status -r ".*"

docs/docs/usage/overview.md

@@ -9,7 +9,7 @@ gut provides a comprehensive set of commands for managing multiple GitHub reposi
 ## Repository Operations
 
 ### clone
-Clone all repositories matching a pattern.
+Clone all repositories matching a pattern. Automatically detects and pulls Git LFS objects for repos that use LFS.
 
 ```bash
 gut clone -o <org> -r "<regex>"
@@ -28,7 +28,7 @@ gut fetch -o <org> -r "<regex>"
 ```
 
 ### pull
-Pull the current branch of all local repositories that match a pattern.
+Pull the current branch of all local repositories that match a pattern. Automatically pulls Git LFS objects for repos that use LFS.
 
 ```bash
 gut pull -o <org> -r "<regex>"
@@ -227,6 +227,79 @@ gut set permission -o <org> -t team-slug \
 
 **Permissions:** `pull`, `push`, `admin`, `maintain`, `triage`
 
+### rename team
+Rename a GitHub organisation team. The new slug is auto-generated by GitHub from the new name.
+
+```bash
+gut rename team <team-slug> <new-name> -o <org>
+```
+
+!!! warning "Team References"
+    Renaming a team may invalidate references in issues and discussions. Requires typing "YES" to confirm.
+
+## Labels
+
+Manage GitHub labels in bulk across repositories.
+
+### label list
+List all labels for repositories matching a pattern.
+
+```bash
+gut label list -o <org> -r "<regex>"
+```
+
+### label create
+Create a label across all matching repositories.
+
+```bash
+gut label create -o <org> -r "<regex>" \
+  --name "bug" --color "d73a4a" \
+  --description "Something isn't working"
+```
+
+### label delete
+Delete a label from all matching repositories.
+
+```bash
+gut label delete -o <org> -r "<regex>" --name "bug"
+```
+
+### label rename
+Rename a label (and optionally update color/description) across all matching repositories.
+
+```bash
+gut label rename -o <org> -r "<regex>" \
+  --name "bug" --new-name "defect" \
+  --color "ff0000"
+```
+
+## Health
+
+### health
+Comprehensive health check for repositories and system configuration.
+
+```bash
+# Check repos for a single owner
+gut health -o <org>
+
+# Check all owners
+gut health --all-owners
+```
+
+**Checks performed:**
+
+- **NFD/NFC normalization**: Filenames with decomposed Unicode that cause conflicts on macOS
+- **Case duplicates**: Files differing only in case (e.g., `File.txt` vs `file.txt`)
+- **Large files**: Files exceeding threshold that should use Git LFS (default: 50 MB)
+- **Long paths**: Filenames/paths exceeding Windows compatibility limits
+- **System config**: Git version, `core.precomposeUnicode`, `core.autocrlf`, Git LFS installation
+
+**Options:**
+
+- `--large-file-mb <SIZE>` — Size threshold in MB for LFS check (default: 50)
+- `--filename-length-bytes <LENGTH>` — Filename length warning threshold (default: 200)
+- `--path-length-bytes <LENGTH>` — Full path length warning threshold (default: 400)
+
 ## Topics
 
 Topics are GitHub repository tags that help organize and discover repositories.
@@ -236,6 +309,9 @@ List topics for all repositories that match a pattern.
 
 ```bash
 gut topic list -o <org> -r "<regex>"
+
+# JSON output
+gut topic list -o <org> -r "<regex>" --json
 ```
 
 ### topic set
@@ -365,18 +441,59 @@ List all repositories matching a pattern.
 gut show repositories -o <org> -r "<regex>"
 ```
 
-### show users
-Show all users in an organization.
+### show repository
+Show detailed access information for a specific repository, including teams and collaborators with permission levels and affiliation.
+
+```bash
+gut show repository <repo-name> -o <org>
+```
+
+**Output:**
+
+- Teams table: Team Slug, Team Name, Permission
+- Collaborators table: Username, Permission, Affiliation (org/direct/outside)
+
+### show access
+Show user access levels across repositories.
+
+```bash
+# Compact view (one column per user)
+gut show access <username1> <username2> -o <org> -r "<regex>"
+
+# Detailed view (one row per user/repo)
+gut show access <username1> -o <org> --long
+```
+
+### show teams
+Show all teams in an organisation.
+
+```bash
+# Flat table
+gut show teams -o <org>
+
+# Hierarchical tree showing parent/child relationships
+gut show teams -o <org> --tree
+```
+
+### show team
+Show details of a specific team including members, repositories, and parent/child teams.
+
+```bash
+gut show team <team-slug> -o <org>
+```
+
+### show members
+Show all members in an organization with their roles and 2FA status.
 
 ```bash
-gut show users -o <org>
+gut show members -o <org>
 ```
 
-### set organisation
-Set the default organization for all commands.
+### set owner
+Set the default owner (organisation or user) for all commands.
 
 ```bash
-gut set organisation <org-name>
+gut set owner <owner-name>
 ```
 
 ## Template System