move bare ref and update links (#93)

* move bare ref and update links

* move pear ref into subfolder

* update README

* tiny fix

---------

Co-authored-by: Vivek Singh <vivek@peartree.to>

reference/pear/cli.md

@@ -0,0 +1,166 @@
+# Command Line Interface (CLI) 
+
+<mark style="background-color: #8484ff;">**experimental**</mark>
+
+The Command Line Interface is the primary interface for Pear Development.
+
+## pear init [dir]
+
+Create initial project files.
+
+```
+--yes|-y         Autoselect all defaults
+--type|-t=type   Project type: desktop (default) or terminal
+--force|-f       Force overwrite existing files
+--with|-w=name   Additional functionality. Available: node
+```
+  
+## pear dev [flags] [dir] [...app-args]
+
+Run a project in development mode from disk.
+
+Alias for: `pear run --dev <dir>`
+
+```
+--link=url                 Simulate deep-link click open
+--store|-s=path            Set the Application Storage path
+--tmp-store|-t             Automatic new tmp folder as store path
+```  
+## pear stage <channel|key> [dir]
+
+Synchronize local changes to key.
+
+Channel name must be specified on first stage,
+in order to generate the initial key.
+
+Outputs diff information and project key.
+
+```
+  --json         Newline delimited JSON output
+  --dry-run|-d   Execute a stage without writing
+  --bare|-b      File data only, no warmup optimization
+  --ignore       Comma separated file path ignore list
+  --name         Advanced. Override app name
+```
+  
+## pear seed <channel|key> [dir]
+
+Seed project or reseed key.
+
+Specify channel or key to seed a project.
+
+Specify a remote key to reseed.
+
+```
+  --json        Newline delimited JSON output
+  --seeders|-s  Additional public keys to seed from
+  --name        Advanced. Override app name
+  --verbose|-v  Additional output
+```
+  
+## pear run [flags] <key|dir|alias> [...app-args]
+
+Run an application from a key or dir.
+
+|       |                                                   |
+|-------|---------------------------------------------------|
+| key   | `pear://<key>`                            |
+| dir   | `file://<absolute-path>` \| `<absolute-path>` \| `<relative-path>` |
+| alias | `pear://<alias>`                          |
+
+
+```
+  --dev                      Enable --devtools & --updates-diff
+  --devtools                 Open devtools with application [Desktop]
+  --updates-diff             Enable diff computation for Pear.updates
+  --no-updates               Disable updates firing via Pear.updates
+  --link=url                 Simulate deep-link click open
+  --store|-s=path            Set the Application Storage path
+  --tmp-store|-t             Automatic new tmp folder as store path
+  --checkout=n               Run a checkout, n is version length
+  --checkout=release         Run checkout from marked released length
+  --checkout=staged          Run checkout from latest version length
+  --no-ask-trust             Exit instead of asking to trust unknown keys
+  --detached                 Wakeup existing app or run detached
+```
+
+### Examples 
+
+```
+pear run pear://u6c6it1hhb5serppr3tghdm96j1gprtesygejzhmhnk5xsse8kmy
+```
+
+```
+pear run -s /tmp/app-storage path/to/an-app-folder some --app args
+```
+
+```
+pear run -t file://path/to/an-app-folder --some app --args
+```
+
+```
+pear run pear://keet
+```
+
+## pear release <channel|key> [dir]
+
+Set production release version.
+
+Set the release pointer against a version (default latest).
+
+Use this to indicate production release points.
+
+```
+  --json                   Newline delimited JSON output
+  --checkout=n|current     Set a custom release length (version)
+```
+  
+## pear info [key]
+
+Read project information.
+
+Supply a key to view application info
+
+Without a key pear info shows Pear info
+
+```
+  --json          Newline delimited JSON output
+```
+  
+## pear dump <key> <dir>
+
+Synchronize files from key to dir.
+
+```
+  --json          Newline delimited JSON output
+  --checkout=n    Dump from a custom release length (version)
+```
+  
+## pear sidecar
+
+The Pear Sidecar is a local-running HTTP and IPC server which
+provides access to corestores.
+
+This command instructs any existing sidecar process to shutdown
+and then becomes the sidecar.
+
+```
+  --mem              memory mode: RAM corestore
+  --attach-boot-io   include initial sidecar I/O (if applicable)
+```
+  
+## pear repl
+
+Connect to a Read-Eval-Print-Loop session with sidecar.
+
+A key is printed out, use with repl-swarm module to connect.
+
+## pear versions
+
+Output version information.
+
+```
+--json        Single JSON object
+```
+  
+