Adjust directories for cleaner use w/Arduino

/system is only downloaded tools
/tools is all scripts/submodules that are part of the main core
/lib is the linker libs

.gitmodules

@@ -5,5 +5,5 @@
 	path = pico-sdk
 	url = https://github.com/raspberrypi/pico-sdk.git
 [submodule "system/pyserial"]
-	path = system/pyserial
+	path = tools/pyserial
 	url = https://github.com/pyserial/pyserial.git

platform.txt

@@ -78,7 +78,7 @@ compiler.S.extra_flags=
 compiler.ar.extra_flags=
 compiler.elf2hex.extra_flags=
 
-discovery.rp2040.pattern="{runtime.tools.pqt-python3.path}/python3" "{runtime.platform.path}/system/discovery.py"
+discovery.rp2040.pattern="{runtime.tools.pqt-python3.path}/python3" "{runtime.platform.path}/tools/discovery.py"
 
 # USB Flags
 # ---------
@@ -106,7 +106,7 @@ archive_file_path={build.path}/{archive_file}
 recipe.ar.pattern="{compiler.path}{compiler.ar.cmd}" {compiler.ar.flags} {compiler.ar.extra_flags} "{archive_file_path}" "{object_file}"
 
 ## Combine gc-sections, archives, and objects
-recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}"  "-L{build.path}" {compiler.c.elf.flags} {compiler.c.elf.extra_flags} "-Wl,--script={build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" --specs=nosys.specs {compiler.ldflags} -o "{build.path}/{build.project_name}.elf" {object_files} "{build.path}/{archive_file}" {runtime.platform.path}/system/libs/pico.a -lm -I{runtime.platform.path}/pico-sdk/src/rp2040/hardware_regs/include/ -I{runtime.platform.path}/pico-sdk/src/common/pico_binary_info/include {runtime.platform.path}/assembly/bs2_default_padded_checksummed.S
+recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}"  "-L{build.path}" {compiler.c.elf.flags} {compiler.c.elf.extra_flags} "-Wl,--script={build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" --specs=nosys.specs {compiler.ldflags} -o "{build.path}/{build.project_name}.elf" {object_files} "{build.path}/{archive_file}" {runtime.platform.path}/lib/pico.a -lm -I{runtime.platform.path}/pico-sdk/src/rp2040/hardware_regs/include/ -I{runtime.platform.path}/pico-sdk/src/common/pico_binary_info/include {runtime.platform.path}/assembly/bs2_default_padded_checksummed.S
 
 ## Create output (UF2 file)
 recipe.objcopy.uf2.pattern="{runtime.tools.pqt-elf2uf2.path}/elf2uf2" "{build.path}/{build.project_name}.elf" "{build.path}/{build.project_name}.uf2"
@@ -133,6 +133,6 @@ tools.uf2conv.upload.protocol=uf2
 tools.uf2conv.upload.params.verbose=
 tools.uf2conv.upload.params.quiet=
 
-tools.uf2conv.upload.pattern="{cmd}" "{runtime.platform.path}/system/uf2conv.py" --serial "{serial.port}" --family RP2040 --deploy "{build.path}/{build.project_name}.uf2"
+tools.uf2conv.upload.pattern="{cmd}" "{runtime.platform.path}/tools/uf2conv.py" --serial "{serial.port}" --family RP2040 --deploy "{build.path}/{build.project_name}.uf2"
-tools.uf2conv.upload.network_pattern="{cmd}" "{runtime.platform.path}/system/uf2conv.py" --serial "{serial.port}" --family RP2040 --deploy "{build.path}/{build.project_name}.uf2"
+tools.uf2conv.upload.network_pattern="{cmd}" "{runtime.platform.path}/tools/uf2conv.py" --serial "{serial.port}" --family RP2040 --deploy "{build.path}/{build.project_name}.uf2"
 

system/placeholder

@@ -0,0 +1 @@
+placeholder

tools/get.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
-# This script will download and extract required tools into the current directory.
+# This script will download and extract required tools into the system directory.
-# Tools list is obtained from package/package_esp8266com_index.template.json file.
+# Originally written by Ivan Grokhotkov, 2015.
-# Written by Ivan Grokhotkov, 2015.
 #
 from __future__ import print_function
 import os
@@ -49,14 +48,17 @@ def report_progress(count, blockSize, totalSize):
         sys.stdout.flush()
 
 def unpack(filename, destination):
+    here = os.getcwd()
     dirname = ''
     print('Extracting {0}'.format(filename))
     if filename.endswith('tar.gz'):
         tfile = tarfile.open(filename, 'r:gz')
+        os.chdir("../system/")
         tfile.extractall(destination)
         dirname= tfile.getnames()[0]
     elif filename.endswith('zip'):
         zfile = zipfile.ZipFile(filename)
+        os.chdir("../system/")
         zfile.extractall(destination)
         dirname = zfile.namelist()[0]
     else:
@@ -69,6 +71,7 @@ def unpack(filename, destination):
         if os.path.isdir(rename_to):
             shutil.rmtree(rename_to)
         shutil.move(dirname, rename_to)
+    os.chdir(here)
 
 def get_tool(tool):
     archive_name = tool['archiveFileName']