restructure: code+libs under src/, runtime resources under data/

Separate the two concerns the repo root was mixing:
- src/   — bs/, modules/, libs/ (code + vendored libs)
- data/  — fpga_registry.yaml, probes.yaml, bsdl_files/, bscan_proxies/,
           scripts/ (everything the tool reads at runtime, CWD-relative)
- doc/   — kept at the root

CMake: repoint DIR_MODULES/DIR_LIBS and add_subdirectory at src/; emit
the binary at the build/ root (build/bs) via CMAKE_RUNTIME_OUTPUT_DIRECTORY
instead of the nested build/src/bs/. The jtag_core ../../libs path still
resolves since modules and libs moved together.

Runtime default paths now point under data/ (fpga.c, probes.c, script.c
bsdl_files lookup, init.c config.script). Docs (README/tutorial/CLAUDE)
updated for the new layout, src/ module paths, and ./build/bs.

Validated on the IGLOO2/FlashPro: profiles, autoinit, and svf_play all
work run from the repo root.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

CMakeLists.txt

@@ -2,6 +2,10 @@ cmake_minimum_required(VERSION 3.10)
 
 project(BoundaryScanExplorer)
 
+# Put the built executable at the build/ root (build/bs), not nested under
+# build/src/bs/ where the source tree would otherwise mirror it.
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+
 # Digilent JTAG-SMT* backend. The driver dlopen's libdjtg/libdmgr at
 # runtime and degrades to "no probe" if they're absent, so building it
 # in costs nothing — default ON. Needs <dlfcn.h>, so UNIX only.
@@ -16,8 +20,8 @@ option(BS_ENABLE_DIGILENT
 
 # script and jtag_core must be the last linked archive for the application to compile
 set(BS_MODULES script jtag_core)
-set(DIR_MODULES ${CMAKE_SOURCE_DIR}/modules)
-set(DIR_LIBS ${CMAKE_SOURCE_DIR}/libs)
+set(DIR_MODULES ${CMAKE_SOURCE_DIR}/src/modules)
+set(DIR_LIBS ${CMAKE_SOURCE_DIR}/src/libs)
 
 # We dive into submodules
 file(GLOB MODULES_DIRS RELATIVE ${DIR_MODULES} ${DIR_MODULES}/*)
@@ -32,10 +36,10 @@ foreach(module ${MODULES_DIRS})
             list(APPEND BS_MODULES ${module})
         endif()
         # We'll compile the module
-        add_subdirectory(modules/${module})
+        add_subdirectory(src/modules/${module})
     else()
         message(STATUS "Ignored   : ${module}")
     endif()
 endforeach()
 
-add_subdirectory(bs)
+add_subdirectory(src/bs)