When exporting my project with org-publish, the exporter generates anchors with names such as "orga79e495" and refers to them when linking to the headers from other files. However, the generated anchor names don't match between files, resulting in all links being dead.
Furthermore, the publishing directory is not respected, so all links still point to the directory that the org file was in, even though the html files are located elsewhere. Example: I have put the files needed to reproduce this at https://gist.github.com/martinhansdk/f81a5fdf340eab591e6df55645cfd22d They can be viewed there or fetched with git: git clone https://gist.github.com/martinhansdk/ f81a5fdf340eab591e6df55645cfd22d Run emacs -Q -l minimal-org.el Then export with M-x org-publish org I get files in the exported/ subdirectory. The last link in the clocking table in exported/time.html is <a href="file:///home/mrhn/bugreports/orgmode-html/ journal.html#org2f3d7f7">Worked on supporting ä, ö, and ü</a> But that should have been <a href="journal.html#org5c71d1e">Worked on supporting ä, ö, and ü</a> Note that both the path is absolute where it should have been relative and the anchor is wrong. As far as I can tell, both problems stem from the fact that the links in the clocking table are absolute file system links. This is, however how the clock table code (org-dblock-update) formats the table. If I manually transform the links in time.org to manual links, then the HTML links are no longer dead. As an aside, is there any way to prevent the following line from appearing in the exported HTML? #+BEGIN: clocktable :scope agenda :link t :maxlevel 5 Thanks, Martin Emacs : GNU Emacs 24.5.1 (x86_64-pc-linux-gnu, GTK+ Version 3.22.11) of 2017-09-12 on hullmann, modified by Debian Package: Org mode version 9.1.3 (9.1.3-2-g322612-elpa @ /home/mrhn/.emacs.d/elpa/org-20171120/) current state: ============== (setq org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate) org-link-file-path-type 'relative org-occur-hook '(org-first-headline-recenter) org-metaup-hook '(org-babel-load-in-session-maybe) org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"] org-latex-format-inlinetask-function 'org-latex-format-inlinetask- default-function org-confirm-shell-link-function 'yes-or-no-p org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default org-latex-format-headline-function 'org-latex-format-headline- default-function org-after-todo-state-change-hook '(org-clock-out-if-current) org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn ## CONTENTS)"] org-odt-format-headline-function 'org-odt-format-headline-default-function org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-mode-hook '(#[0 "\300\301\302\303\304$\207" [add-hook change-major-mode-hook org-show-block-all append local] 5 "\n\n(fn)"] #[0 "\300\301\302\303\304$\207" [add-hook change-major-mode-hook org-babel-show-result-all append local] 5 "\n\n(fn)"] org-babel-result-hide-spec org-babel-hide-all-hashes) org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn ENTRY)"] org-archive-hook '(org-attach-archive-delete-maybe) org-ascii-format-drawer-function #[771 "\207" [] 4 "\n\n(fn NAME CONTENTS WIDTH)"] org-odt-format-inlinetask-function 'org-odt-format-inlinetask- default-function org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-confirm-elisp-link-function 'yes-or-no-p org-metadown-hook '(org-babel-pop-to-session-maybe) org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"] org-html-format-headline-function 'org-html-format-headline- default-function org-link-parameters '(("id" :follow org-id-open) ("rmail" :follow org-rmail-open :store org-rmail-store-link) ("mhe" :follow org-mhe-open :store org-mhe-store-link) ("irc" :follow org-irc-visit :store org-irc-store-link) ("info" :follow org-info-open :export org-info-export :store org-info-store-link) ("gnus" :follow org-gnus-open :store org-gnus-store-link) ("docview" :follow org-docview-open :export org-docview-export :store org-docview-store-link) ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link) ("bbdb" :follow org-bbdb-open :export org-bbdb-export :complete org-bbdb-complete-link :store org-bbdb-store-link) ("w3m" :store org-w3m-store-link) ("file+sys") ("file+emacs") ("doi" :follow org--open-doi-link) ("elisp" :follow org--open-elisp-link) ("file" :complete org-file-complete-link) ("ftp" :follow (lambda (path) (browse-url (concat "ftp:" path)))) ("help" :follow org--open-help-link) ("http" :follow (lambda (path) (browse-url (concat "http:" path)))) ("https" :follow (lambda (path) (browse-url (concat "https:" path)))) ("mailto" :follow (lambda (path) (browse-url (concat "mailto:"; path)))) ("news" :follow (lambda (path) (browse-url (concat "news:"; path)))) ("shell" :follow org--open-shell-link)) org-html-format-inlinetask-function 'org-html-format-inlinetask- default-function org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-publish-project-alist '(("org-notes" :base-directory "." :base-extension "org" :publishing-directory "exported/" :recursive t :publishing-function org-html-publish-to-html :headline-levels 4 :auto-preamble t) ("org-static" :base-directory "." :base-extension "css\\|js\\|png\\|jpg\\|gif\\|pdf\\|mp3\\|ogg\\|swf" :publishing-directory "exported/" :recursive t :publishing-function org-publish-attachment) ("org" :components ("org-notes" "org-static"))) )
