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I have 2 mesa_git recipes and one .bbappend:
./meta-webos/recipes-graphics/mesa/mesa_git.bbappend
./meta-webos-backports/recipes-graphics/mesa/mesa_git.bb
./oe-core/meta/recipes-graphics/mesa/mesa_9.0.2.bb
./oe-core/meta/recipes-graphics/mesa/mesa_git.bb

0001-configure-Avoid-use-of-AC_CHECK_FILE-for-cross-compi.patch is only in meta-webos-backports layer
oe-core is dylan release which doesn't have it yet (that's why we have backports layer)
./meta-webos-backports/recipes-graphics/mesa/mesa/0001-configure-Avoid-use-of-AC_CHECK_FILE-for-cross-compi.patch

do_fetch finds it correctly:
bitbake -e mesa | grep ^FILESPATH= | sed "s/\"/\n/g; s/:/\n/g"
FILESPATH=
/OE/meta-webos/recipes-graphics/mesa/mesa/i586
/OE/meta-webos/recipes-graphics/mesa/mesa/x86
/OE/meta-webos/recipes-graphics/mesa/mesa/qemuall
/OE/meta-webos/recipes-graphics/mesa/mesa/qemux86
/OE/meta-webos/recipes-graphics/mesa/mesa/webos
/OE/meta-webos/recipes-graphics/mesa/mesa/
/OE/meta-webos-backports/recipes-graphics/mesa/mesa-9.1.3+gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/i586
/OE/meta-webos-backports/recipes-graphics/mesa/mesa-9.1.3+gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/x86
/OE/meta-webos-backports/recipes-graphics/mesa/mesa-9.1.3+gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/qemuall
/OE/meta-webos-backports/recipes-graphics/mesa/mesa-9.1.3+gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/qemux86
/OE/meta-webos-backports/recipes-graphics/mesa/mesa-9.1.3+gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/webos
/OE/meta-webos-backports/recipes-graphics/mesa/mesa-9.1.3+gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/
/OE/meta-webos-backports/recipes-graphics/mesa/mesa/i586
/OE/meta-webos-backports/recipes-graphics/mesa/mesa/x86
/OE/meta-webos-backports/recipes-graphics/mesa/mesa/qemuall
/OE/meta-webos-backports/recipes-graphics/mesa/mesa/qemux86
/OE/meta-webos-backports/recipes-graphics/mesa/mesa/webos
/OE/meta-webos-backports/recipes-graphics/mesa/mesa/
/OE/meta-webos-backports/recipes-graphics/mesa/files/i586
/OE/meta-webos-backports/recipes-graphics/mesa/files/x86
/OE/meta-webos-backports/recipes-graphics/mesa/files/qemuall
/OE/meta-webos-backports/recipes-graphics/mesa/files/qemux86
/OE/meta-webos-backports/recipes-graphics/mesa/files/webos
/OE/meta-webos-backports/recipes-graphics/mesa/files/

bitbake -DDD mesa:
DEBUG: Searching for 0001-configure-Avoid-use-of-AC_CHECK_FILE-for-cross-compi.patch in paths:
    /OE/meta-webos/recipes-graphics/mesa/mesa/i586
    /OE/meta-webos/recipes-graphics/mesa/mesa/x86
    /OE/meta-webos/recipes-graphics/mesa/mesa/qemuall
    /OE/meta-webos/recipes-graphics/mesa/mesa/qemux86
    /OE/meta-webos/recipes-graphics/mesa/mesa/webos
    /OE/meta-webos/recipes-graphics/mesa/mesa/
    /OE/oe-core/meta/recipes-graphics/mesa/mesa-9.1~gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/i586
    /OE/oe-core/meta/recipes-graphics/mesa/mesa-9.1~gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/x86
    /OE/oe-core/meta/recipes-graphics/mesa/mesa-9.1~gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/qemuall
    /OE/oe-core/meta/recipes-graphics/mesa/mesa-9.1~gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/qemux86
    /OE/oe-core/meta/recipes-graphics/mesa/mesa-9.1~gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/webos
    /OE/oe-core/meta/recipes-graphics/mesa/mesa-9.1~gitAUTOINC+b3f1f665b0fef178ae193e6b111f14c9a5ad3b25/
    /OE/oe-core/meta/recipes-graphics/mesa/mesa/i586
    /OE/oe-core/meta/recipes-graphics/mesa/mesa/x86
    /OE/oe-core/meta/recipes-graphics/mesa/mesa/qemuall
    /OE/oe-core/meta/recipes-graphics/mesa/mesa/qemux86
    /OE/oe-core/meta/recipes-graphics/mesa/mesa/webos
    /OE/oe-core/meta/recipes-graphics/mesa/mesa/
    /OE/oe-core/meta/recipes-graphics/mesa/files/i586
    /OE/oe-core/meta/recipes-graphics/mesa/files/x86
    /OE/oe-core/meta/recipes-graphics/mesa/files/qemuall
    /OE/oe-core/meta/recipes-graphics/mesa/files/qemux86
    /OE/oe-core/meta/recipes-graphics/mesa/files/webos
    /OE/oe-core/meta/recipes-graphics/mesa/files/
DEBUG: Defaulting to /OE/downloads/0001-configure-Avoid-use-of-AC_CHECK_FILE-for-cross-compi.patch for 0001-configure-Avoid-use-of-AC_CHECK_FILE-for-cross-compi.patch
WARNING: Unable to get checksum for mesa SRC_URI entry 0001-configure-Avoid-use-of-AC_CHECK_FILE-for-cross-compi.patch: file could not be found