Update shared apache config to match newer deployments and phylesystem-api

[jimallman]

Currently testing these changes as a hot-fix on ot50 (devapi). We need identical changes to a number of URL rewrites from (dev)api to (dev)phylesystemapi:

    # Explicit routing for /cached/* URLs (in phylesystem-api)

    RewriteEngine on
    #WAS RewriteRule ^/cached/(.*) "https://devphylesystemapi.opentreeoflife.org/phylesystem/default/cached/$1" [P]
    RewriteRule ^/cached/(.*) "https://devphylesystemapi.opentreeoflife.org/cached/$1" [P]

    # Avoid pyramids/web2py conflicts by deploying phylesystem_api on a different machine, and rewriting urls (wthout redirect)
    SSLProxyEngine On
    RewriteEngine on
    #WAS RewriteRule "^/v3/study(.*)"                "https://devphylesystemapi.opentreeoflife.org/phylesystem/v1/study$1" [P]
    #WAS RewriteRule "^/v3/phylesystem_config"       "https://devphylesystemapi.opentreeoflife.org/phylesystem/v1/phylesystem_config" [P]
    #WAS RewriteRule "^/v3/render_markdown"          "https://devphylesystemapi.opentreeoflife.org/phylesystem/v1/render_markdown" [P]
    #WAS RewriteRule "^/v3/trees_in_synth"           "https://devphylesystemapi.opentreeoflife.org/phylesystem/v1/trees_in_synth" [P]
    #WAS RewriteRule "^/v3/include_tree_in_synth"    "https://devphylesystemapi.opentreeoflife.org/phylesystem/v1/include_tree_in_synth" [P]
    #WAS RewriteRule "^/v3/exclude_tree_from_synth"  "https://devphylesystemapi.opentreeoflife.org/phylesystem/v1/exclude_tree_from_synth" [P]
    RewriteRule "^/v3/study(.*)"                "https://devphylesystemapi.opentreeoflife.org/v1/study$1" [P]
    RewriteRule "^/v3/phylesystem_config"       "https://devphylesystemapi.opentreeoflife.org/v1/phylesystem_config" [P]
    RewriteRule "^/v3/render_markdown"          "https://devphylesystemapi.opentreeoflife.org/v1/render_markdown" [P]
    RewriteRule "^/v3/trees_in_synth"           "https://devphylesystemapi.opentreeoflife.org/v1/trees_in_synth" [P]
    RewriteRule "^/v3/include_tree_in_synth"    "https://devphylesystemapi.opentreeoflife.org/v1/include_tree_in_synth" [P]
    RewriteRule "^/v3/exclude_tree_from_synth"  "https://devphylesystemapi.opentreeoflife.org/v1/exclude_tree_from_synth" [P]

Also, make the same change (strip phylesystem/ from URLs) for misc. methods for
- collections
- amendments
- utility methods