Ensure all commands in compilation_commands.json use absolute paths. (#3415)

* Fix resolving of absolute path for toolchain

By placing the `where_is_program` call into this function, all references to the compiler will be made absolute, instead of just ones in the top environment. Previously, all references to the compiler for user source code would not use the full path in the compilation database, which broke `clangd`'s detection of system includes.

* Linting issue

platformio/builder/tools/compilation_db.py

@@ -76,6 +76,16 @@ def makeEmitCompilationDbEntry(comstr):
         :return: target(s), source(s)
         """
 
+        # Resolve absolute path of toolchain
+        for cmd in ("CC", "CXX", "AS"):
+            if cmd not in env:
+                continue
+            if os.path.isabs(env[cmd]):
+                continue
+            env[cmd] = where_is_program(
+                env.subst("$%s" % cmd), env.subst("${ENV['PATH']}")
+            )
+
         dbtarget = __CompilationDbNode(source)
 
         entry = env.__COMPILATIONDB_Entry(
@@ -195,14 +205,6 @@ def generate(env, **kwargs):
     )
 
     def CompilationDatabase(env, target):
-        # Resolve absolute path of toolchain
-        for cmd in ("CC", "CXX", "AS"):
-            if cmd not in env:
-                continue
-            env[cmd] = where_is_program(
-                env.subst("$%s" % cmd), env.subst("${ENV['PATH']}")
-            )
-
         result = env.__COMPILATIONDB_Database(target=target, source=[])
 
         env.AlwaysBuild(result)