docs(cli): replace legacy flag examples with cobra subcommands (rq)

5 files changed, 62 insertions, 61 deletions

diff --git a/doc/README.md b/doc/README.md
index 02ea0f0..1391062 100644
--- a/doc/README.md
+++ b/doc/README.md
@@ -29,6 +29,6 @@ GitSyncer is a tool for synchronizing Git repositories across multiple platforms
 
 1. Install GitSyncer
 2. Create a configuration file
-3. Run `gitsyncer --sync-all` to sync all configured repositories
+3. Run `gitsyncer sync all` to sync all configured repositories
 
-See the [Configuration Guide](configuration.md) for detailed setup instructions.
\ No newline at end of file
+See the [Configuration Guide](configuration.md) for detailed setup instructions.
diff --git a/doc/api-reference.md b/doc/api-reference.md
index b7ed2f8..7ad41b1 100644
--- a/doc/api-reference.md
+++ b/doc/api-reference.md
@@ -73,16 +73,16 @@ Lists all configured organizations from config.
 Lists all configured repositories from config.
 
 #### func HandleSync(cfg *config.Config, flags *Flags) int
-Synchronizes a single repository specified by `--sync` flag.
+Synchronizes a single repository, used by `gitsyncer sync repo [name]`.
 
 #### func HandleSyncAll(cfg *config.Config, flags *Flags) int
-Synchronizes all repositories listed in configuration.
+Synchronizes all repositories listed in configuration, used by `gitsyncer sync all`.
 
 #### func HandleSyncCodebergPublic(cfg *config.Config, flags *Flags) int
-Discovers and syncs all public Codeberg repositories to other platforms.
+Discovers and syncs all public Codeberg repositories to other platforms, used by `gitsyncer sync codeberg-to-github`.
 
 #### func HandleSyncGitHubPublic(cfg *config.Config, flags *Flags) int
-Discovers and syncs all public GitHub repositories to other platforms.
+Discovers and syncs all public GitHub repositories to other platforms, used by `gitsyncer sync github-to-codeberg`.
 
 ### Helper Functions (sync_handlers.go)
 
diff --git a/doc/configuration.md b/doc/configuration.md
index 230cac6..922d089 100644
--- a/doc/configuration.md
+++ b/doc/configuration.md
@@ -63,7 +63,7 @@ Array of organization objects. At least one organization must be configured.
   - Can also be set via environment variable or file
 
 #### repositories (optional)
-Array of repository names to sync. If empty, use `--sync-codeberg-public` or `--sync-github-public` to discover repositories.
+Array of repository names to sync. If empty, use `gitsyncer sync codeberg-to-github` or `gitsyncer sync github-to-codeberg` to discover repositories.
 
 #### exclude_branches (optional)
 Array of regex patterns for branches to exclude from synchronization.
@@ -174,7 +174,7 @@ Sync between GitHub and Codeberg:
 ## GitHub Token Configuration
 
 GitHub tokens are required for:
-- Creating repositories (`--create-github-repos`)
+- Creating repositories (`sync ... --create-repos`)
 - Listing private repositories
 - Higher API rate limits
 
@@ -211,7 +211,7 @@ GitHub tokens are required for:
 #### Method 2: Environment Variable
 ```bash
 export GITHUB_TOKEN="ghp_xxxxxxxxxxxx"
-gitsyncer --sync-all
+gitsyncer sync all
 ```
 
 #### Method 3: Token File
@@ -223,13 +223,13 @@ chmod 600 ~/.gitsyncer_github_token
 ### Testing Token
 
 ```bash
-gitsyncer --test-github-token
+gitsyncer test github-token
 ```
 
 ## Codeberg Token Configuration
 
 Codeberg tokens are required for:
-- Creating repositories (`--create-codeberg-repos`)
+- Creating repositories (`sync ... --create-repos`)
 - Listing private repositories
 
 ### Token Sources (in order of precedence)
@@ -264,7 +264,7 @@ Codeberg tokens are required for:
 #### Method 2: Environment Variable
 ```bash
 export CODEBERG_TOKEN="xxxxxxxxxxxx"
-gitsyncer --sync-all
+gitsyncer sync all
 ```
 
 #### Method 3: Token File
@@ -289,7 +289,7 @@ The `exclude_branches` field accepts regular expressions to filter out branches
 
 To see which branches are excluded:
 ```bash
-gitsyncer --sync repo-name
+gitsyncer sync repo repo-name
 # Output will show excluded branches and patterns
 ```
 
@@ -301,7 +301,7 @@ Begin with a minimal configuration and add complexity as needed.
 ### 2. Use Dry Run
 Test your configuration with `--dry-run` before actual synchronization:
 ```bash
-gitsyncer --sync-all --dry-run
+gitsyncer sync all --dry-run
 ```
 
 ### 3. Secure Your Tokens
@@ -322,7 +322,7 @@ gitsyncer --sync-all --dry-run
 
 ### Configuration Not Found
 ```bash
-$ gitsyncer --sync myrepo
+$ gitsyncer sync repo myrepo
 No configuration file found. Please create one of:
   - ./gitsyncer.json
   - /home/user/.config/gitsyncer/config.json
@@ -333,7 +333,7 @@ No configuration file found. Please create one of:
 
 ### Invalid JSON
 ```bash
-$ gitsyncer --list-orgs
+$ gitsyncer list orgs
 Failed to load configuration: invalid character '}' looking for beginning of object key string
 ```
 
@@ -341,7 +341,7 @@ Failed to load configuration: invalid character '}' looking for beginning of obj
 
 ### No Organizations Configured
 ```bash
-$ gitsyncer --sync myrepo
+$ gitsyncer sync repo myrepo
 Configuration must have at least one organization
 ```
 
@@ -349,7 +349,7 @@ Configuration must have at least one organization
 
 ### Token Issues
 ```bash
-$ gitsyncer --test-github-token
+$ gitsyncer test github-token
 ERROR: Token test failed: authentication failed (401)
 ```
 
diff --git a/doc/development.md b/doc/development.md
index 0d80958..9aa7454 100644
--- a/doc/development.md
+++ b/doc/development.md
@@ -351,7 +351,7 @@ test: add integration tests for branch filtering
    cd test && ./run_integration_tests.sh
    
    # Test manually
-   ./gitsyncer --sync test-repo
+   ./gitsyncer sync repo test-repo
    ```
 
 2. **Format code**:
@@ -414,7 +414,7 @@ func (s *Syncer) debugOperation() {
 
 Use:
 ```bash
-GITSYNCER_DEBUG=1 gitsyncer --sync test-repo
+GITSYNCER_DEBUG=1 gitsyncer sync repo test-repo
 ```
 
 ### Common Issues
diff --git a/doc/examples.md b/doc/examples.md
index 4f8dba4..7d01fd8 100644
--- a/doc/examples.md
+++ b/doc/examples.md
@@ -16,36 +16,36 @@ This guide provides practical examples of using GitSyncer for various scenarios.
 
 ```bash
 # Sync a specific repository
-gitsyncer --sync my-project
+gitsyncer sync repo my-project
 
 # Sync with custom working directory
-gitsyncer --sync my-project --work-dir /tmp/gitsyncer-work
+gitsyncer sync repo my-project --work-dir /tmp/gitsyncer-work
 
 # Dry run to preview changes
-gitsyncer --sync my-project --dry-run
+gitsyncer sync repo my-project --dry-run
 ```
 
 ### Sync All Configured Repositories
 
 ```bash
 # Sync all repositories in config
-gitsyncer --sync-all
+gitsyncer sync all
 
-# Create missing GitHub repos automatically
-gitsyncer --sync-all --create-github-repos
+# Create missing repositories automatically
+gitsyncer sync all --create-repos
 ```
 
 ### List Operations
 
 ```bash
 # List configured organizations
-gitsyncer --list-orgs
+gitsyncer list orgs
 
 # List configured repositories
-gitsyncer --list-repos
+gitsyncer list repos
 
 # Show version
-gitsyncer --version
+gitsyncer version
 ```
 
 ## Repository Discovery
@@ -54,33 +54,34 @@ gitsyncer --version
 
 ```bash
 # Discover and sync all public repos from Codeberg
-gitsyncer --sync-codeberg-public
+gitsyncer sync codeberg-to-github
 
 # Also create repos on GitHub if they don't exist
-gitsyncer --sync-codeberg-public --create-github-repos
+gitsyncer sync codeberg-to-github --create-repos
 
 # Dry run to see what would be synced
-gitsyncer --sync-codeberg-public --dry-run
+gitsyncer sync codeberg-to-github --dry-run
 ```
 
 ### Sync All Public GitHub Repositories to Codeberg
 
 ```bash
 # Discover and sync all public repos from GitHub
-gitsyncer --sync-github-public
+gitsyncer sync github-to-codeberg
 
-# Note: Codeberg repos must already exist
-gitsyncer --sync-github-public
+# Also create missing repositories automatically
+gitsyncer sync github-to-codeberg --create-repos
 ```
 
 ### Full Bidirectional Sync
 
 ```bash
 # Sync all public repos in both directions
-gitsyncer --full
+gitsyncer sync bidirectional
 
 # Equivalent to:
-# gitsyncer --sync-codeberg-public --sync-github-public --create-github-repos
+# gitsyncer sync codeberg-to-github --create-repos
+# gitsyncer sync github-to-codeberg --create-repos
 ```
 
 ## Advanced Synchronization
@@ -105,7 +106,7 @@ Configuration with branch exclusions:
 
 Output shows excluded branches:
 ```bash
-$ gitsyncer --sync my-project
+$ gitsyncer sync repo my-project
 
 🚫 Excluded 3 branches based on patterns:
    Patterns: '^temp-', '^feature/experimental-', '-wip$'
@@ -119,7 +120,7 @@ $ gitsyncer --sync my-project
 
 When conflicts occur:
 ```bash
-$ gitsyncer --sync my-project
+$ gitsyncer sync repo my-project
 
 ERROR: repository has unresolved merge conflicts
 Please resolve conflicts in: /home/user/.gitsyncer-work/my-project
@@ -135,18 +136,18 @@ git status
 git add .
 git commit -m "Resolved conflicts"
 cd -
-gitsyncer --sync my-project
+gitsyncer sync repo my-project
 
 # Option 2: Start fresh
 rm -rf /home/user/.gitsyncer-work/my-project
-gitsyncer --sync my-project
+gitsyncer sync repo my-project
 ```
 
 ### Abandoned Branch Detection
 
 GitSyncer detects branches inactive for 6+ months:
 ```bash
-$ gitsyncer --sync-all
+$ gitsyncer sync all
 
 [1/3] Syncing project1...
 Repository project1 synchronized successfully!
@@ -172,10 +173,10 @@ Repository: project1
 ```bash
 # Add to crontab (crontab -e)
 # Sync all repos every 6 hours
-0 */6 * * * /usr/local/bin/gitsyncer --sync-all --config /home/user/.gitsyncer.json >> /var/log/gitsyncer.log 2>&1
+0 */6 * * * /usr/local/bin/gitsyncer sync all --config /home/user/.gitsyncer.json >> /var/log/gitsyncer.log 2>&1
 
 # Sync public repos daily at 2 AM
-0 2 * * * /usr/local/bin/gitsyncer --full >> /var/log/gitsyncer-public.log 2>&1
+0 2 * * * /usr/local/bin/gitsyncer sync bidirectional >> /var/log/gitsyncer-public.log 2>&1
 ```
 
 ### Shell Script Wrapper
@@ -192,13 +193,13 @@ LOG_FILE="$HOME/.gitsyncer/sync.log"
 echo "Starting sync at $(date)" >> "$LOG_FILE"
 
 # Test GitHub token first
-if ! gitsyncer --test-github-token; then
+if ! gitsyncer test github-token; then
     echo "GitHub token test failed" >> "$LOG_FILE"
     exit 1
 fi
 
 # Sync all repos
-if gitsyncer --sync-all --config "$CONFIG_FILE" >> "$LOG_FILE" 2>&1; then
+if gitsyncer sync all --config "$CONFIG_FILE" >> "$LOG_FILE" 2>&1; then
     echo "Sync completed successfully at $(date)" >> "$LOG_FILE"
 else
     echo "Sync failed at $(date)" >> "$LOG_FILE"
@@ -243,7 +244,7 @@ jobs:
       - name: Sync repositories
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: gitsyncer --sync-all --create-github-repos
+        run: gitsyncer sync all --create-repos
 ```
 
 ## Troubleshooting Scenarios
@@ -252,7 +253,7 @@ jobs:
 
 ```bash
 # Test token is valid
-$ gitsyncer --test-github-token
+$ gitsyncer test github-token
 Testing GitHub token authentication...
   Loaded token from env var (length: 40)
   Checking URL: https://api.github.com/repos/myorg/gitsyncer
@@ -279,7 +280,7 @@ git reflog
 ### Repository Not Found
 
 ```bash
-$ gitsyncer --sync nonexistent-repo
+$ gitsyncer sync repo nonexistent-repo
 ERROR: Failed to clone from any organization
 ```
 
@@ -292,34 +293,34 @@ Solutions:
 
 ```bash
 # Permission denied
-$ gitsyncer --sync my-project --work-dir /root/work
+$ gitsyncer sync repo my-project --work-dir /root/work
 ERROR: failed to create work directory: permission denied
 
 # Solution: Use accessible directory
-gitsyncer --sync my-project --work-dir ~/gitsyncer-work
+gitsyncer sync repo my-project --work-dir ~/gitsyncer-work
 
 # Disk space issues
-$ gitsyncer --sync large-repo
+$ gitsyncer sync repo large-repo
 ERROR: write error: no space left on device
 
 # Solution: Clean up or use different disk
 df -h
 rm -rf ~/.gitsyncer-work/old-repo
-gitsyncer --sync large-repo --work-dir /mnt/storage/gitsyncer
+gitsyncer sync repo large-repo --work-dir /mnt/storage/gitsyncer
 ```
 
 ### Network and Connectivity
 
 ```bash
 # SSH key issues
-$ gitsyncer --sync my-project
+$ gitsyncer sync repo my-project
 ERROR: git@github.com: Permission denied (publickey)
 
 # Solution: Add SSH key to agent
 ssh-add ~/.ssh/id_rsa
 
 # Firewall/proxy issues
-$ gitsyncer --sync my-project
+$ gitsyncer sync repo my-project
 ERROR: Failed to connect to github.com port 22: Connection timed out
 
 # Solution: Use HTTPS URLs in config
@@ -336,20 +337,20 @@ ERROR: Failed to connect to github.com port 22: Connection timed out
 ### 1. Start with Dry Run
 Always test with `--dry-run` first:
 ```bash
-gitsyncer --sync-all --dry-run
+gitsyncer sync all --dry-run
 ```
 
 ### 2. Use Specific Working Directories
 Organize syncs by project or purpose:
 ```bash
-gitsyncer --sync personal-projects --work-dir ~/sync/personal
-gitsyncer --sync work-projects --work-dir ~/sync/work
+gitsyncer sync repo personal-projects --work-dir ~/sync/personal
+gitsyncer sync repo work-projects --work-dir ~/sync/work
 ```
 
 ### 3. Monitor Sync Operations
 Keep logs for troubleshooting:
 ```bash
-gitsyncer --sync-all 2>&1 | tee -a ~/gitsyncer.log
+gitsyncer sync all 2>&1 | tee -a ~/gitsyncer.log
 ```
 
 ### 4. Regular Maintenance
@@ -369,5 +370,5 @@ gitsyncer --config config-with-token.json
 
 # Good
 export GITHUB_TOKEN="$(pass show github/token)"
-gitsyncer --sync-all
-```
\ No newline at end of file
+gitsyncer sync all
+```